great choice for engines. I'm also smack in the middle of a 97 explorer engine into my 86 vert. Several things that have to be changed, and I'll start there.
-all accessories, and timing cover, swap your 5.0 stuff onto it.
-oil pan, pump, pickup tube, swap the mustang stuff onto it.
a few things. The valve springs and cam are low revving truck parts. At a minimum, swap HO mustang valves onto the explorer engine. I'm going with some tfs springs, and 1.7 roller rockers. The explorer engine works well with a HO mustang cam, or you can go aftermarket. My brothers explorer engine is getting the tfs springs, tfs stage one cam, and 1.6 roller rockers, to be sure it doesn't have interference, piston to valve wise.
97 was a cutover year. Mine has the gt40p's, but, strangely enough, has the intake from 96, that has the internal egr ports that will make me smog legal for cali. Starting in 97 sometime, the intakes stopped having internal egr ports. you'll know when you pull your upper and lower apart, and see a hole right in the center. If it's there, you got the egr intake that's compatible with smog for a mustang, if not, it's not technically smog legal.
you'll have the gt40's, or the gt40's, both great heads. Mine has the P heads. I chose the frpp ceramic coated shorty headers from summit for $299. (stainless are a little cheaper) ALL ford headers are P head compliant.
your heads will have 4 bars, and GTP, as shown in my pictures, or three bars for gt40 heads. Best of luck, and ask me if you need any help at all.