Nice beginning of a build list. Although there are some areas I'd work on before dropping the pulley.
Your exhaust manifolds, ported or not...the front is a bad restriction. Headers would help bring your heat down. Currently you are likely heating up because of backpressure at the manifolds. Many here like TOGS, I'm not a fan and they are no longer produced. Therefore finding them is tougher. SLP or some of the SLP knockoffs are great and can be had new for ~$300. Tough to beat.
Next restriction is the heads.
Injectors: On a Gen V and a cam you are moving enough air that you should be running out of injector around the 3.2" pulley mark. It sounds like you are in the mindset that I call pulley envy. A bit more timing and a larger pulley can net you much more power than simply stacking boost in the LIM. Stacking pressure in the LIM creates a lot of heat.
Pounding on your car cold is horrible. The main reason you are likely faster when cold is because your knock sensors are not active until you reach ~160F. If you have knock once you are warmed up..please understand that it'* also there when cold, but the pcm isn't reading the sensors. This is a potential motor blowing situation.
O2'*, running the O2'* in the 1000mV area at WOT is extremely rich and costing you a good amount of power. At your mod level you should be tuning the car and using a wide band O2 for monitoring your fueling. Narrow band sensors are very inaccurate and only a starting point for low level modding.
A 2.25" core would fit if you added ZZP'* throttle body turn down adapter.
Iridium spark plugs: Iridium plugs last longer because they are a harder metal that doesn't break down quickly. The downside is that they retain heat much more than a standard cheap copper plug. With your mods, it would seem you should be running 2-3 ranges colder, say a Autolite 104 or 103. This would reduce knock and temps in the motor.
ZZP PCM: I've got very few comments about the pcm except there are forums with stickies saying "if you want to blow your motor, buy a ZZP pcm." With the fueling etc that you are seeing, it'* pretty clear it'* time to custom tune. Doesn't matter which vendor pcm you have...it wouldn't be adequate so it'* not something we can suggest one vendor or another to do. Custom tune done on your car for your car is the way to get the best and safest reliable power for your mods.
Radiator: IIRC there'* a Caddy around 04 that uses the same sizing, but thicker core. I used RadiatorBarn.com and just fllipped through the various cars to locate one that was the same height and width with outlets in the same places as the Bonneville to locate one that would work.
Hope this helps out not only with your question...but to help you gain more power from your current mods.
00 Regal GS: All kinds of cool stuff.