The very first thing a convertible needs before any engine rework is subframe connector rails. Properly done, they will stiffen up the body, improve handling and reduce the squeaks and rattles common to most convertibles.
The long tube headers have clearance problems with some cars. In some cases it is ground clearance and with others it is interference between the steering shaft and header tubes.
Some Ford Racing stainless steel short tube headers are your best bet for fit, finish and quality. They are also smog legal everyplace with the possible exception of California.
http://www.summitracing.com/parts/fms-m-9430-p50/overview/make/ford
On a budget? do the junkyard upgrade...
94-95 Mustang GT MAF - $40-$100. It is 70 MM instead of the stock 55 MM on regular stangs built prior to 94. It uses a slip on duct on the side that goes to the throttle body and a 4 bolt flange on the other. You need a flange adapter to fit the stock slip on air ducting that goes to the air box. Wiring plugs right in with no changes. *1 *2
95-97 Ford Explorer intake manifold & throttle body $150-$300. The intake manifold flows 220 CFM +, much better than stock. Throttle body is 65 MM, bigger than the 60 MM on stock stangs. I got a 1996 with EGR passages that match the stock setup, so my smog gear works just like factory. You’ll need a 65 MM EGR spacer & new gaskets for $65-$90 so you have a place to mount the EGR & throttle linkage.
Explorer GT40 or GT 40P cylinder heads. The GT40 heads have 3 bars cast at the end of the head. GT 40 's will work with any header setup, they are found on the earlier model Explorers from 95 - 97 I believe. The GT 40P's are found on 98-2001 model cars and have 4 bars cast into the end of the cylinder head.. They need aftermarket headers designed to clear the angled spark plugs.
Whatever you GT$0 heads get, plan to replace the valve springs replaced with good quality aftermarket springs from someplace like Crane Cams or Competition Cams.
3G alternator from 94-95 Mustangs or other Ford. $20-$120. A must have to make the electrical system work like it should or if you have an electric fan. You’ll need a 4 gauge power wire and a 125-135 amp fuse to go with it about $15- $30.
Lincoln MK VIII electric fan -$40-$160. Free up some HP by not having to drive the stock fan. The 3G alternator upgrade is a must have prerequisite before you do the MK VIII fan. You won’t have enough electrical power if you don’t do the 3G upgrade.
*1.) Metal flange adapter
http://www.kustomz.com/components.html Buy the TR70 for $40. Or spend some time on eBay looking for one that may fit.
*2.) MAF & sensor interchange
The 94-95 Mustang 5.0 MAF & sensor is also found on:
1995-94 Mustang 3.8L F2VF-12B579-A2A,
1994-92 Crown Victoria 4.6L F2VF-12B579-A2A,
1995-94 Mustang, Mustang Cobra 5.0L F2VF-12B579-A2A,
1994-92 Town Car 4.6L F2VF-12B579-A2A,
1994-92 Grand Marquis 4.6L F2VF-12B579-A2A,
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.