So the first thing I would do it find out why the car has a Bama chip on it. It may be that the previous owner just thought it would be a good idea and bought a canned tune i.e. no dyno time just one of their tunes based on a sheet you fill out. You may be able to call Bama and see if they can tell you about the chip based on a serial number or something. Where I am heading with this is you may be able to just remove it and not put it back on. I would also contact them and see what it would cost to tune it again based on what you decide to do. I have no experience with them so do some research.
The reason for possibly reusing the Bama chip for me would be to install a 1996 to 2001 GT Mustang 80mm MAF and then some 24 or 30 lb/hr injectors. Bama should know the stock transfer function for the MAF and be able to modify the fuel tables for the larger injectors. This is preferred over a MAF that is "calibrated" for larger injectors but a calibrated MAF will work just fine. 24's or 30's will be fine and I ran 42's for years on my mild 302 as I knew I was going to step up to a stroker and did not want to buy once. I would say that if you are going to tune the car then 24's, 30's, 36's, or 42's will all work just depends on what you can find for the best price. If you are going to go the calibrated MAF route I would go either 24's or 30's. That is just me as my experience with calibrated and larger injectors has been very hit and miss.
So with all of that said I would go with the AFR 165’s, Explorer upper and lower (have TMoss port the lower), call Comp Cams and have them recommend a cam (should be able to reuse the stock lifters but check them over), and you will need to check push rods for correct length. You will need to decide if you are going to run the stock pedestal rockers, aftermarket pedestal rockers, or stud mount roller rockers. Stock pedestals are good for about 0.500" of lift as determined by Jay Allen who used to be in the custom grind camshaft business. He also mentions that aftermarket pedestals are good to about 0.550" lift. You also need to consult with your cam provider of choice as to what they recommend and what ratio which is typically 1.6:1. If you go aftermarket then I would suggest Scorpion or Hartland Sharp as they are both still made in the USA. Comp Cams may or may not be but my guess is they have migrated offshore. There may be more so do your research.
Thread on how to plumb the vacuum lines for an Explorer intake:
Have seen this question asked a million times. So here's a diagram. This is an EARLY Explorer intake with the EGR port. There were two lower manifolds. The RF-F87E-9K461-BA lower was early and had the bosses present for the ACT. The RF-F87E-9K461-BB lower was later (non-EGR) and lacks the...
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I would also run a cold air kit that puts the air filter in the inner fender. Depending on what MAF you decide to go with you may need an adapter for the inlet side. Several CAI's out there so do the research. I run an 2000GT 80mm MAF and use an adapter. This is how I reworked the
BBK cold air kit I had on my car as it was a restriction on the 331:
So many years ago I bought a BBK cold air induction kit (CAI) in chrome and it has hung around on the car since then. At that time it was bought and installed the car a 75mm Pro-M Bullet MAF so the kit worked pretty well. Several years down the road I sold the Pro-M and 24 lb/hr injectors...
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From here you need to run at least a 65mm throttle body which you can rob off an Explorer or get an Accufab unit ($$$ but nice pieces). Here is a write up on how to modify the Explorer TB to work on our cars:
This will be a few parts, as I make a little progress. I already have a converted explorer TB on my car but it's a later version with the enlarged TPS sensor mount. So anyway, here we are. Explorer on left, stock mustang on right. You can see the difference in the throttle linkage...
stangnet.com
So now you have the induction on the car to your liking, good intakes, good heads, good cam and now you need fuel. If the car is still running a stock fuel pump or if you do not know the history on it I would drop the fuel tank and put a 190 log Walbro pump in (LMR has them for a decent price) and change the fuel filter while you are at it. Now the fuel system is good to go unless you just want to put an adjustable FPR on it but I doubt it will need one.
The car will eventually need a good 2.5" exhaust on it but it will run with whatever is on there.
Rear gears...man oh man. There will be all kinds of opinions on this and whoever you choose to get the cam from will absolutely need to know what gears you are going to run. I have had 3.73's in my Coupe for about 20 years and with the stock T5 first gear is pretty much worthless in that I shift out of it as soon as the car starts moving. I will be moving to 3.55's or 3.31's at some point very soon.
So I know this was a lot but planning an engine build or just doing a head, cam, and intake swap needs to be planned and you need to know your budget and then work within it.