Driveshafts: On 4wd's, they are the same. On 2wd's, I honestly can't say so take this with a grain of sale: I would think the trans are the same length, same spline count which means the shafts should be the same too.
Floorplate: I'd grab one made for a manual. That way it has all your screw holes for the floor plastics and stuff. Pull it from any 98+ with a manual...they're the same.
Crossmembers: 98+ torsion bar's are all the same x-member and trans mount. 98+ coil springs are the same as well. My brothers '01 4cyl manual xmember is the same xmember that my buddy Casper's '98 6cyl auto.
Harness: Get a (preferably) same year, same engine, same drive(2wd) but manual trans engine/trans harness. It's all one piece and is easiest for swap...Just unclip your stock harness from the PCM to the big square connector that mates the PCM to the interior wiring(can't remember the damn name but the connector is C110 in the ford electrical manual), and all engine sensors/pigtails/etc. Then clip in the manual harness to the engine and the trans, done! Don't forget your similar year/same engine/manual trans PCM too! Your year won't require a reflash for PATS because you don't have it....so you'll be able to do your swap, and drive it away and not pay the dealer about $150 for a flash!
I've got links for both my local buddy's auto-to-manual swap threads...but can't find 'em at the moment. I'll link when I find 'em. Tons of info packed into it including all the small BS parts you'll need. *note: both these trucks are 4.0 4x4's. But alot of the ideas and info applies to you.