diff --git a/src/deprecations.jl b/src/deprecations.jl
index 3735d8f6f4..6e8ea23b1c 100644
--- a/src/deprecations.jl
+++ b/src/deprecations.jl
@@ -12,7 +12,9 @@ end
 const ODESystem = IntermediateDeprecationSystem
 
 function IntermediateDeprecationSystem(args...; kwargs...)
-    Base.depwarn("`ODESystem(args...; kwargs...)` is deprecated. Use `System(args...; kwargs...) instead`.", :ODESystem)
+    Base.depwarn(
+        "`ODESystem(args...; kwargs...)` is deprecated. Use `System(args...; kwargs...) instead`.",
+        :ODESystem)
 
     return System(args...; kwargs...)
 end
diff --git a/src/inputoutput.jl b/src/inputoutput.jl
index 6a17f76d80..6563ac678f 100644
--- a/src/inputoutput.jl
+++ b/src/inputoutput.jl
@@ -200,7 +200,7 @@ function generate_control_function(sys::AbstractSystem, inputs = unbound_inputs(
         eval_module = @__MODULE__,
         kwargs...)
     isempty(inputs) && @warn("No unbound inputs were found in system.")
-    if !iscomplete(sys)
+    if !isscheduled(sys)
         sys = mtkcompile(sys; inputs, disturbance_inputs)
     end
     if disturbance_inputs !== nothing
diff --git a/src/linearization.jl b/src/linearization.jl
index 327381d611..dc6eeedaaa 100644
--- a/src/linearization.jl
+++ b/src/linearization.jl
@@ -565,6 +565,50 @@ function linearize_symbolic(sys::AbstractSystem, inputs,
     (; A, B, C, D, f_x, f_z, g_x, g_z, f_u, g_u, h_x, h_z, h_u), sys
 end
 
+struct IONotFoundError <: Exception
+    variant::String
+    sysname::Symbol
+    not_found::Any
+end
+
+function Base.showerror(io::IO, err::IONotFoundError)
+    println(io,
+        "The following $(err.variant) provided to `mtkcompile` were not found in the system:")
+    maybe_namespace_issue = false
+    for var in err.not_found
+        println(io, "  ", var)
+        if hasname(var) && startswith(string(getname(var)), string(err.sysname))
+            maybe_namespace_issue = true
+        end
+    end
+    if maybe_namespace_issue
+        println(io, """
+        Some of the missing variables are namespaced with the name of the system \
+        `$(err.sysname)` passed to `mtkcompile`. This may be indicative of a namespacing \
+        issue. `mtkcompile` requires that the $(err.variant) provided are not namespaced \
+        with the name of the root system. This issue can occur when using `getproperty` \
+        to access the variables passed as $(err.variant). For example:
+
+        ```julia
+        @named sys = MyModel()
+        inputs = [sys.input_var]
+        mtkcompile(sys; inputs)
+        ```
+
+        Here, `mtkcompile` expects the input to be named `input_var`, but since `sys`
+        performs namespacing, it will be named `sys$(NAMESPACE_SEPARATOR)input_var`. To \
+        fix this issue, namespacing can be temporarily disabled:
+
+        ```julia
+        @named sys = MyModel()
+        sys_nns = toggle_namespacing(sys, false)
+        inputs = [sys_nns.input_var]
+        mtkcompile(sys; inputs)
+        ```
+        """)
+    end
+end
+
 """
 Modify the variable metadata of system variables to indicate which ones are inputs, outputs, and disturbances. Needed for `inputs`, `outputs`, `disturbances`, `unbound_inputs`, `unbound_outputs` to return the proper subsets.
 """
@@ -605,19 +649,16 @@ function markio!(state, orig_inputs, inputs, outputs, disturbances; check = true
     if check
         ikeys = keys(filter(!last, inputset))
         if !isempty(ikeys)
-            error(
-                "Some specified inputs were not found in system. The following variables were not found ",
-                ikeys)
+            throw(IONotFoundError("inputs", nameof(state.sys), ikeys))
         end
         dkeys = keys(filter(!last, disturbanceset))
         if !isempty(dkeys)
-            error(
-                "Specified disturbance inputs were not found in system. The following variables were not found ",
-                ikeys)
+            throw(IONotFoundError("disturbance inputs", nameof(state.sys), ikeys))
+        end
+        okeys = keys(filter(!last, outputset))
+        if !isempty(okeys)
+            throw(IONotFoundError("outputs", nameof(state.sys), okeys))
         end
-        (all(values(outputset)) || error(
-            "Some specified outputs were not found in system. The following Dict indicates the found variables ",
-            outputset))
     end
     state, orig_inputs
 end
diff --git a/src/systems/abstractsystem.jl b/src/systems/abstractsystem.jl
index e4e696934c..e40fa9a017 100644
--- a/src/systems/abstractsystem.jl
+++ b/src/systems/abstractsystem.jl
@@ -652,6 +652,8 @@ function complete(
         # Ideally we'd do `get_ps` but if `flatten = false`
         # we don't get all of them. So we call `parameters`.
         all_ps = parameters(sys; initial_parameters = true)
+        # inputs have to be maintained in a specific order
+        input_vars = inputs(sys)
         if !isempty(all_ps)
             # reorder parameters by portions
             ps_split = reorder_parameters(sys, all_ps)
@@ -670,6 +672,12 @@ function complete(
             end
             ordered_ps = vcat(
                 ordered_ps, reduce(vcat, ps_split; init = eltype(ordered_ps)[]))
+            if isscheduled(sys)
+                # ensure inputs are sorted
+                input_idxs = findfirst.(isequal.(input_vars), (ordered_ps,))
+                @assert all(!isnothing, input_idxs)
+                @assert issorted(input_idxs)
+            end
             @set! sys.ps = ordered_ps
         end
     elseif has_index_cache(sys)
diff --git a/src/systems/index_cache.jl b/src/systems/index_cache.jl
index e006da3cb5..b57412bf2e 100644
--- a/src/systems/index_cache.jl
+++ b/src/systems/index_cache.jl
@@ -97,8 +97,8 @@ function IndexCache(sys::AbstractSystem)
         end
     end
 
-    tunable_buffers = Dict{Any, Set{BasicSymbolic}}()
-    initial_param_buffers = Dict{Any, Set{BasicSymbolic}}()
+    tunable_pars = BasicSymbolic[]
+    initial_pars = BasicSymbolic[]
     constant_buffers = Dict{Any, Set{BasicSymbolic}}()
     nonnumeric_buffers = Dict{Any, Set{SymbolicParam}}()
 
@@ -107,6 +107,10 @@ function IndexCache(sys::AbstractSystem)
         buf = get!(buffers, ctype, S())
         push!(buf, sym)
     end
+    function insert_by_type!(buffers::Vector{BasicSymbolic}, sym, ctype)
+        sym = unwrap(sym)
+        push!(buffers, sym)
+    end
 
     disc_param_callbacks = Dict{SymbolicParam, Set{Int}}()
     events = vcat(continuous_events(sys), discrete_events(sys))
@@ -210,9 +214,9 @@ function IndexCache(sys::AbstractSystem)
                     ctype <: AbstractArray{Real} ||
                     ctype <: AbstractArray{<:AbstractFloat})
                     if iscall(p) && operation(p) isa Initial
-                        initial_param_buffers
+                        initial_pars
                     else
-                        tunable_buffers
+                        tunable_pars
                     end
                 else
                     constant_buffers
@@ -255,47 +259,41 @@ function IndexCache(sys::AbstractSystem)
 
     tunable_idxs = TunableIndexMap()
     tunable_buffer_size = 0
-    bufferlist = is_initializesystem(sys) ? (tunable_buffers, initial_param_buffers) :
-                 (tunable_buffers,)
-    for buffers in bufferlist
-        for (i, (_, buf)) in enumerate(buffers)
-            for (j, p) in enumerate(buf)
-                idx = if size(p) == ()
-                    tunable_buffer_size + 1
-                else
-                    reshape(
-                        (tunable_buffer_size + 1):(tunable_buffer_size + length(p)), size(p))
-                end
-                tunable_buffer_size += length(p)
-                tunable_idxs[p] = idx
-                tunable_idxs[default_toterm(p)] = idx
-                if hasname(p) && (!iscall(p) || operation(p) !== getindex)
-                    symbol_to_variable[getname(p)] = p
-                    symbol_to_variable[getname(default_toterm(p))] = p
-                end
-            end
+    if is_initializesystem(sys)
+        append!(tunable_pars, initial_pars)
+        empty!(initial_pars)
+    end
+    for p in tunable_pars
+        idx = if size(p) == ()
+            tunable_buffer_size + 1
+        else
+            reshape(
+                (tunable_buffer_size + 1):(tunable_buffer_size + length(p)), size(p))
+        end
+        tunable_buffer_size += length(p)
+        tunable_idxs[p] = idx
+        tunable_idxs[default_toterm(p)] = idx
+        if hasname(p) && (!iscall(p) || operation(p) !== getindex)
+            symbol_to_variable[getname(p)] = p
+            symbol_to_variable[getname(default_toterm(p))] = p
         end
     end
 
     initials_idxs = TunableIndexMap()
     initials_buffer_size = 0
-    if !is_initializesystem(sys)
-        for (i, (_, buf)) in enumerate(initial_param_buffers)
-            for (j, p) in enumerate(buf)
-                idx = if size(p) == ()
-                    initials_buffer_size + 1
-                else
-                    reshape(
-                        (initials_buffer_size + 1):(initials_buffer_size + length(p)), size(p))
-                end
-                initials_buffer_size += length(p)
-                initials_idxs[p] = idx
-                initials_idxs[default_toterm(p)] = idx
-                if hasname(p) && (!iscall(p) || operation(p) !== getindex)
-                    symbol_to_variable[getname(p)] = p
-                    symbol_to_variable[getname(default_toterm(p))] = p
-                end
-            end
+    for p in initial_pars
+        idx = if size(p) == ()
+            initials_buffer_size + 1
+        else
+            reshape(
+                (initials_buffer_size + 1):(initials_buffer_size + length(p)), size(p))
+        end
+        initials_buffer_size += length(p)
+        initials_idxs[p] = idx
+        initials_idxs[default_toterm(p)] = idx
+        if hasname(p) && (!iscall(p) || operation(p) !== getindex)
+            symbol_to_variable[getname(p)] = p
+            symbol_to_variable[getname(default_toterm(p))] = p
         end
     end
 
diff --git a/test/linearize.jl b/test/linearize.jl
index 668ba68c13..1e5fd29016 100644
--- a/test/linearize.jl
+++ b/test/linearize.jl
@@ -151,12 +151,12 @@ lsys = ModelingToolkit.reorder_unknowns(lsys, desired_order, reverse(desired_ord
 @test lsys.D == [4400 -4400]
 
 ## Test that there is a warning when input is misspecified
-@test_throws "Some specified inputs were not found" linearize(pid,
+@test_throws ["inputs provided to `mtkcompile`", "not found"] linearize(pid,
     [
         pid.reference.u,
         pid.measurement.u
     ], [ctr_output.u])
-@test_throws "Some specified outputs were not found" linearize(pid,
+@test_throws ["outputs provided to `mtkcompile`", "not found"] linearize(pid,
     [
         reference.u,
         measurement.u