The stock computer will adapt to all kinds of modifications without any reprogramming. Only when you get into really wild heads/intake manifold/cam combinations is a custom tune or chip needed for smooth street performance.
The 70 MM MAF concerns me: there are a limited number of 70 MM Ford MAFs that match the stock computer's programing.
Here's the list of compatible 70 MM Ford MAFs:
MAF & sensor interchange
1994-95 Mustang 5.0 MAF & F2VF-12B579-A2A sensor
1995-94 Mustang 3.8L, F2VF-12B579-A2A sensor
1994-92 Crown Victoria 4.6L, F2VF-12B579-A2A sensor
1995-94 Mustang, Mustang Cobra 5.0L, F2VF-12B579-A2A sensor
1994-92 Town Car 4.6L, F2VF-12B579-A2A sensor
1994-92 Grand Marquis 4.6L, F2VF-12B579-A2A sensor
Only the F2VF-12B579-xxx sensor used with one of the above 70 MM housings will match the 5.0 Mustang's stock computer. Evidently the –A1A, -A2A, AA, etc. on the end of the part number is a minor variant that did not change the operating specs. You should be able to ignore it and have everything work good.