Nice car. You have 3.73s. Which honestly are junk for these cars. Problem #1. You need 4.10s minimum. Although 4.30s or 4.56s would be better. 4.10s are for 2v N/A cars. 4.30s or higher for N/A 4vs. It's strange adjusting to the early 4vs. They are dogs below 3500. Although they wake up fast. And once you get the hang of it and if you gear it properly, the lack of low end is not even noticeable.
Definitely do the tune up. Do not use anything other than Ford parts for tune up. Don't buy knock off wires, don't dont buy knock off fuel filter, don't buy aftermarket coil packs, etc. Plug wise use a basic copper of your choise gapped @.054. Don't let the auto parts guy con you into buying a platinum. Waste of money.
As far as tuning, the QH is nice. But the handhelds for these are a godsend.
And yes, the IMRC's could be causing an issue. If new the to the 96-98 4v's. Look for cables behind the intake that criss cross. Rev the car and see if they move. (Even if they move it could be a problem) But it gives an idea.
Crawl under and get a picture of the exhaust. I hate a crappy sounding 4v. It's common for people to go cheapass and buy like a pypes violator catback and they are god awful.
I pretty much live, eat, and breath the mod motors. If you need any help or advice feel free to bother me about it. lol.
Nice ride though! I miss my White 98 Cobra.