Ok...I had a big long reply typed in, then got the BSOD...the Blue Screen Of Death!!!
Basically, I think you are running a little lean...Putting the K&N on is getting more air into the motor making it run leaner...
You need to also do the IAC reset procedure explained somewhere on the Gnttype website...get the IAC numbers to about 25-35 in park, when in gear they will be a little lower...
If you haven't already put an aftermarket fuel pump(Walbro 307 or 340) and an adjustable fuel pressure regulator, you need to do that next BEFORE you put a new chip in...The stock pump was barely able to keep up with the stock setup...The stock fuel pressure should be around 38# or so(if my memory is right)...You need a little more...When you put in the Thrasher, you need to raise it to 45#...Fuel system has to be done first on these cars before you do anything else to them...
The miss at medium/WOT, in my opinion, is from detonation(i.e., running a little lean)...
Have you tried the tap test on the MAF??? With the handle of a screwdriver and the car at idle, gently tap(not hard), and did I mention not hard, on your MAF...If the idle stumbles or misses, then the MAF is probably bad...Good Luck finding a new one...But I really think you are just running out of fuel...
The stock chip also has a little too aggressive timing curve for the gas we've got today...If you can, with TLink hooked up, drive around until you notice the miss and look on TLink and see if you're getting knock retard at that time...Running a little lean and having the stock chip on 92-93 octane pump gas is dangerous...
Hope this helps...
Anyone else with something to add???