IMO, putting an aftermarket intake on but leaving the stock MAF and TB is not worth the money, time, and effort. If you want to leave the stock heads on at least put an explorer 65MM TB and a 94-95 Mustang 70MM MAF on. You can also save some $$$$ by simply swapping on the entire explorer U/L intake, TB, and EGR plate on. You can get that for around $100 from most junkyards and modify the TB to work.
Just because the motor is 20 years old does not mean you need a rebuild. Are you burning oil, losing water? Have you checked the plugs, compression or done a leakdown test? When was the last time it was tuned? How many miles on the car. It is not uncommon for maintained 5.0's to go well over 100k miles, even with forced induction or spray.
That being said, first determine what you want to do with the car - DD, street strip, strip only, N/A, blower, etc. and that should determine your course of action. Too many times people start throwing parts on their cars and wonder why they either run like crap or do not meet their expectations. For about 3-400 bucks. you can pull the entire top end off an explorer- heads, intake, TB etc, and swap out the springs on the heads, and have a nice little car that gets about 260-280 hp. If you want to step up to the next level, TW makes a great top end kit for about $2500 that includes everything- heads, TB, cam, intake,timing chain, head bolts, gaskets that is a proven 330-350 hp swap. If you are dead set on a new motor, a good cheap one is the ford 340hp crate motor for about $3500. You'll need to add the intake, tb, maf etc.. but that is a nice little motor for the price .
Again, figure out what your plans are. Remember the more HP you make. the more things brake and the other parts you will need to support that HP - injectors, fuel pump, MAF, clutch, transmission, cooling, brakes, etc.
just my .02