It sounds like you are more than half the problem to be honest. You are pushing too far with mods and likely you have more KR than a motor with a bad lower end. Going on the cut to the chase, we don't care where your shifts happen etc, they should occur where the pcm tells them. If not, tell us about the problem, not how things changed slightly as you modded.
Let's start off simple here.
1. You feel you read alot, get used to it. I'm all about teaching someone about the car and not handing them answers without understanding. You'll fish when I'm done with you.
2. Tell us all your mods. We like brand names and model etc...like which plugs you are running and what they are gapped to, last tune up, etc etc. I don't like to read a ton to solve things either..sometimes it's the details that matter.
3. Pull out the scanner and monitor KR. Likely you'll see a ton when the car acts powerless.
4. Clear the cat code, does it come right back within two or three drive cycles.
5. How do your front bank 1 O2 readings look? Always rich?
To clarify my pushing too far comment. 1.9's w/o springs may be fine when the car has 30K on it as the springs haven't weakened, likely you don't have 30K and your springs are pathetic, add boost and change the valvetrain a bit, hello valve float. Your springs can't gain muscle by working harder etc, they just get worse over time.
3.2 pulley, on rockers alone this is too much pulley envy. Too many people have tested this in the past and learned that there simply isn't a reason to use a 3.2. Your motor can't process that much air, so instead you end up spinning the charger fast which generates more heat and heat causes predetonation in the cylinders. Right..your choice of pulley is costing you power. More pressure building up in teh LIM (where the boost reading is taken) does not mean more power from the engine.