High idle sounds like a small air leak still, or maybe your new throttle is allowing more air through when shut than the Puma throttle did.
The throttle should have two things that affect that. The first is a small hole drilled in the throttle plate, the second is an adjustable stop screw on the throttle that prevents the plate from jamming shut into the aluminum body.
You can check the adjusting screw visually, just make sure its set to close completely without jamming into the aluminum too hard. While your inspecting it, you can experiment with the throttle plate hole by placing a piece of strong tape over the hole, then trying the car and see if the idle is correct or not. If its correct, the permanent fix is to put a screw through that hole.
If the throttle is not the culprit, than you either have a leak or the IACV itself isn't quite letting the right flow through. Unfortunately, off the shelf IACV's seem to be hit or miss quality.
One way to compensate is to install a home-made orifice in the IACV supply line. Use a copper or PVC pipe cap that fits exactly inside the IACV supply hose, and drill a small hole in it to allow air flow. Test that out, and adjust orifice hole size as needed until your happy with the performance.
As for the flat spot, your PCM should be more than capable of adjusting itself for a new throttle, I wouldn't spend money on a tune for that. More likely is that the throttle capacity now exceeds the capacity of the intake manifold or some other portion of the system and 5K is pretty close to your max airflow limit right now.
The first thing to rule out is your air filter. Try making a run with the air filter and box removed completely. I know that's scary, just don't do it on gravel or in a dirty environment. If the flat spot is gone, its time for a better filter setup. If the flat spot isn't gone, the first thing to dummy check is that the plumbing and MAF are at least as big as the throttle. If any portion of the system is smaller than the throttle, than that piece becomes your limiting factor. Assuming the plumbing is good, the most likely next culprit is the intake manifold itself, for which there are limited options short of a custom build or an FRP manifold.
The other oddball that could be throwing a wrench into your works is fuel. I would think the pump should be adequate for any bolt-on mod, but your fuel filter may be dirty enough that it cant really pass enough flow at the high RPM's.
