Hmmmmmm....Lets check a few things....these are just ideas, things to throw on a plate and chew on. Ok there are a couple of things to look at.
1. I noticed you had the Bosch plugs in. Did you look at them to see what condition they were in when you started experiencing this problem? Specifically check the gapping and any abnormalities.

2. Have you made any adjustments to the intake? Check the clamps and see if any are loose.

3. Have a friend get in the car and slowly bring the RPM up and listen for the changes you noticed and see if you hear a possible vacuum leak.

Think backwards on everything you have done for the past few weeks/months and see if maybe something got mixed up, tossed up...you know....

Also, start the car at night. Run the engine till operating temp comes up and look at the exhaust manifold. If it is glowing red that is bad. You have replaced the cat. If they glow, that is an indication of a....I forget...lean/rich mixture and sometimes crops up when your cat has died. Happened on my cavalier....quite a scary thing.

Maybe your timing is slightly off...

Well I hope this gets you started! Wish I could have said "Hey I'll fix it for ya!"......
Give us the heads up as you run thru the diagnostics.

ALSO do a computer code scan and see if you find anything out of the ordinary.

Rich


'96 Mystique, Zetec, MTX.
---Mods---
Removed both intake resonators and airbox. Installed APC air filter and APC crankcase ventilation filter. Removed exhaust resonator.
Installed XM Satellite Radio. Replaced bad alternator and 175a fusible link...much fun!
Intake plenum---GONE!!!!
My car growls louder than yours.
If I can't buy it, I'll build it...Trust Me!!!!