ok... just wrapping up a 4-month ordeal doing my engine swap.
1. Iron-block = 80+lbs of added weight to a pig heavy SUV.. especially if its AWD.. Just sayin...
2. I can speak to '02-'03 vs '04-05 EXPLORER aluminum engines. pretty much everything outside the long block and intake is totally different. harness, EGR, TB, fuel rails, PVC, etc etc etc.
So with that said: Put your "new" engine on a stand. Set your old engine on a tire or another stand and literally strip the "NEW" engine down to bare intake and leave the front dress. Now, just take each part from the old engine, move it over. injectors, fuel rail, coil packs, EGR, Elbow, TB, etc...
The knock sensors are the other challenge. You can safely drill and tap the bosses just go slowly and and be sure to have the right tap on hand. Just go carefully.
3. putting it all back together: Be sure to have the starter/power/alt harness hanging DOWN!!! talk about a mutha to fix once its all in... just did that tonight... 2 hours of fighting to get the harness down past the pass. side engine mount.
4. The radiator/Trans cooler/condenser set up is Bass-Akwards Stupid engineering... go to your local body shop/paint supply place, get some clips that are called "u-nuts" they slip over the sheet metal and act like a nut on the back side. Basically you need to reverse engineer the entire Rad-trans cooler-condeser assembly so that everything bolts from the engine side FORWARD so that you aren't fighting putting it all back together... STUPID design.. First time in 30 years working on Ford's I screamed "WTF! did Ford higher someone from GM to design this!??!!??!
5. Anti-freeze: Ford Yellow is NOT required since you're starting fresh.
good luck... I'm finishing mine this weekend.
Rob