still can't get rid of misfire!

Have you put a scanner on there to make sure you aren't getting any codes. I have a 97 GT Vert and she's been known to throw codes without triggering the CEL. I had the exact problem you are having along with a short in the PCM wiring. You want to talk about a PITA!!! Don't give up man. I got mine straightened out and I know very little about cars.

Also, noticed that you have a PI Intake... Did you use adaptor plates or rtv? Could be blown RTV... have you made sure your TPS is reading right? If you are getting spark, which I think with everything that you've done you should be

Ever since I upgraded my CAI, tb and plenum anytime I disconnect the battery I have to go through the entire process of disconnecting the IAC and letting the car restablish idle.. if i don't it misfires and acceleration sucks..

DO NOT TOUCH THE GAS PEDAL!!

What you will need: a mutlimeter, a big screw phillips screwdriver and some sort of small metal piercing tool
What will be handy but not necessary: an extra set of hands, a scan tool that will give you live data readings. you can rent one from O'Reillys or Autzone.

You will probably get a million different responses on how to do this. This is how I have done it and it works for me. And I've done it a lot. Refer to short in PCM wiring

1. Disconnect the negative terminal to your battery and turn on your headlights for about 10 minutes(there's a lot of speculation as to how long. some people will even say to disconnect the positive terminal and some people will say to leave it disconnected over night.)
2. Disconnect the wiring harness connector to the IAC
3. Turn off headlights and reconnect battery. DO NOT TOUCH THE GAS PEDAL!!
4. (People will probably argue over this step) DO NOT TOUCH THE GAS PEDAL!! Try to start the car. If the car won't start adjust the set screw on the throttle body a 1/4 - 1/2 turn and try again. Repeat until the car will stay running. It will run rough but that is what you want. (some people will say to turn the set screw a few turns before starting your car then turn it down until the car idles at 700rpm or so then)
5. Either way you go let the car sit and idle (DO NOT TOUCH THE GAS PEDAL!!!) until the car reaches operating temperature which to me is when the needle moves to the right leg of the letter 'N'
6. DO NOT TOUCH THE GAS PEDAL!!! Step 5 allows the computer to relearn idle settings. It's pretty cool when you follow my procedure because you can actually hear and feel the car figuring out the proper idle settings. It will go from idling rough to idling smooth as it warms up. Once the car is warmed up verify that the car is idling at around 700rpm. (this is where the scan tool comes in handy cause you can be more accurat but eye-balling it works too) If the car is not adjust the screw until it hits ~700rpm and then let is sit maybe another 10 minutes DO NOT TOUCH THE GAS PEDAL!!!

DO NOT TOUCH THE GAS PEDAL!!!

Turn the car off. Reattach IAC wiring harness. Now some people out there will tell you that this step is not necessary but I totally disagree. Remember we adjusted the set screw on the throttle body. That means that the voltage reading from the TPS sensor has changed. It should read between .96 and .99 volts. (someone correct me if I am wrong) Anything outside of that range will cause all sorts of issues including misfires and rough idle.

7. Now this part you may want to look up and verify before you go piercing wires. What I do is I stick the middle wire with a metal pin, a heavy sewing needle works pretty good (I think, it may be the top wire if you are viewing the connector while still connected) some people just peel off a piece of plastic wire cover because they have to do this so often.

8. Set your multimeter to volts. Turn your car to key, on engine off. then place your positive lead of your mutlimeter on the metal pin and your negative to some ground point. If it comes up as a negative that is okay as long as you are -.96 to -.99. If you get this reading then great you are done and hopefully your issues are gone. If not procede to step 9

9. This is where and extra pair of hands come in handy. Using a large screw driver you will need to loosen the bolts that hold the TPS. DO NOT USE A SCREWDRIVER THAT IS TOO SMALL BECAUSE YOU WILL STRIP THE BOLTS. They probably will be really tight so you have to really lean on the screwdriver and use some finesse. They will come off. Just don't try to turn the bolt all at once or you will strip it. A lot people have broken their TPS from being too rough with these bolts. Again, I'm not a mechanic by any means but just use some common sense.

10. Once the bolts are loose you will need to move the TPS up or down and continue to read the voltage. Once you get it to the desired setting you can retighten the bolts. What I do is I find .97 and then as carefully as possible I tighten the TPS down. what will happen is the voltage will change usually to
.96 or .98 but that it okay. Once you are done with this manually open the throttle body a few times and close it then reread the voltage and make sure it is still withing our desired range.

11. You should be good. I would put a little putty on the whole you made with the pin. Drink a dozen beers or so and crank you car. DO NOT TOUCH THE GAS PEDAL!! I would give the car a once over, make sure nothing came loose while you were messing around under the hood. Let the car idle for a few minutes then take her for a spin. You may want to wait on the dozen beers.

I hope this helps and fixes your problem. Like I said I had a similar issue and it turned out to be a cobination of a bad set of MSD wires only a few months old and a bad TPS. Shortly after that my EGR valve S%^T the bed and then my car developed a short in the lead wire for the PCM effectively resetting the computer every time it blew a fuse. But, I hopefully have it all fixed now. My car has been running smooth with the exception of a slight misfire due to some corrosion on one of the spark plug wires. I cleaned the connectors and have been golden since.