The footboards stay put, you should have a template to cut out the stirrup to make room for the case relocate and the hoses.
The chaincase cup is a necessity, it closes off the hole where the chaincase sticks down and is now vulnerable to damage.
The suspension bolts... get the sled on a strap or something hanging from your ceiling or a cherry picker, find a way to get the skid pulled back in the track so it's fairly tight and then lower your sled down onto the skid to the front bolt is about 1-1/2" or so up from the running board, make some marks for the rear brackets and the front holes, lift the sled up high enough to work under there with a straight edge and find somewhere to measure from and make sure the holes on both sides are in the same spot and drill. Mine ended up being right on the edge of the front mount so I put another plate in beside it and riveted in there good so there was something other than just the tunnel to support it. Mount your rear plates and drop it back down over the skid and bolt it together. Your bolt location in the front could be different, just get it set in place and look it over and see how it looks, not too high/not too low.... hard to explain.
The kits I always use are the Bentwrench kit so if your using something different, results may vary slightly.
You can run the stock 9 toothers with just the 2 inner ones just fine, with the smaller drivers you have to run your track tighter to prevent ratcheting from going around the tighter diameter and 4 drivers are best in that situation but with the D&R you should be just fine with the 2.