1. 4.10 R&P instead of 4.30 R&P on '98-'02: This along with the 5-speed makes a great 4.88 candidate. Downside is on '00+ you may want to add a rear locker (front ARB should be a given on any 100 that will see off-road use IMO).
2. Yes (except for Slee's Blueberry

)
3. OME, Fox, Bilstein are your choices for longer shocks. OME springs and t-bars. You can get about 3-3.5" lift on the rear of a 100 and about 2.75"-3" max lift in front (assuming you install Carl's UCA's and Fox shock to gain droop). I also advise installing a 10-12mm body lift as it is: #1) Cheap; #2): Easy; #3) Eliminates any rear tire rubbing with 35". If you don't run 285 width 35" (Toyo offers their OC AT and MT in 285R75 18" now) you will need to either adjust your turn stops or run wheel spacers up front.