Jeremy,
The axle pads you can get just about any where about $20 (currie, summit racing, etc...)
Covers- you can get a steel cover to replace the composite from Ford $30- $40 I think, but the best bet is the Aluminum covers with the bearing cap preload bolts that are avail for 125-150 from Ford motorsport, Summit, JEGs and a bunch of others. Do a search of this site for the discussion about the breakage at moab and the ARB- some info on the reason for the cover.
Spacers - I dont think the stock lugs are long enough to let you use spacer larger than 5/16"-3/8". You can get longer studs though from just about anyone.
The 8.8 axle is very popular since its been used in pick-ups, stangs, explorers, rangers. Currie Enterprises even uses the parts to make high pinion front axles-and rear, for the relatively weak( when used for moderate wheeling) stock axles that Jeep uses.