Up to you, both systems have strong points. Being a 331 stroker won't make a difference between the two systems.
Mustang system has more bolt on parts and off the shelf tuning options. Explorer system is a little more difficult to wire up, but has EDIS and transmission controls (if you are keeping the 4R70W). From my understanding the Explorer's EEC-V systems is more difficult, but more capable than the Mustang's EEC-IV from a tuning standpoint. Between the 331 and blower you'll need custom tuning, EEC-V has been around for 20 years so most custom tuners can handle it by now.
28 vs 50 oz is a source of confusion and frustration for many SBF owners. A 28oz can be rebuilt as a 50oz and vice-versa with the correct parts. Generally, with the exception of the Explorer and it's weird balancer, a 50 oz engine can be swapped with a 28oz engine. 28oz parts are more common because between the 302 and 351 it was used a lot longer than 50oz. It's more common in the performance aftermarket for the same reason, plus it allows for a stronger crank. You can't find much out there for performance using the Explorer's harmonic balancer, because the Explorer is the only place that it was used. If it had been used in the Mustang (or maybe even F-150) there would be aftermarket 28oz versions everywhere, but performance aftermarket doesn't care about a top heavy SUV.
If you want to build your Explorer 302 into a 331 and use the Explorer's EFI the Damperdudes balancer is a good option. Those stroker kits will replace the stock 50oz crankshaft with an aftermarket 28oz crankshaft. Combine that with the DamperDudes 28oz Explorer balancer and the appropriate 28oz flexplate or flywheel, your engine is now 28oz balance instead of 50oz and you are set to go. That reminds me I should probably buy one to stick on the shelf for a future engine build.
FWIW the DamperDudes balancer isn't limited 302 based stroker kits. If you think you can squeeze in a 351w or even a 427 stroker and want to run it off an Explorer EFI, the DamperDudes unit is what you need. Of course if you build a 427 stroker and want to run it off any stock EFI system, you might need to get you head examined. What ever you do don't let them know you plan to install it in a Ranger, you might not like the padded room they put you in.