Welcome to WF
The choice is really yours as to owning a modded TJ or a modded JK.... money and time are your only setbacks.
1. 31x10.50's ... no spacers needed. Maybe a slight mod to turnlocks by adding washers to them if you rub.
2. IMHO... 4" lift and 33x12.50's on 15x8 wheels with 3.75" Backspacing look best... the way the TJ should have come off the showroom floor. There are plenty of threads on lifts... from $500 to $2500 and all have reviews and stories.
3. I like my Goodyear Duratracs for all around use.... Great off road, quiet on the street, GREAT in the snow and ice. BFG A/T's are a better choice for you since you won't be going off pavement much... if at all.
4. LOL.... well... you can do a HEMI swap.... add a supercharger.. or buy all the hyped up stuff that looks and sounds good, but really does nothing for performance. Header will add a little flow, not much.... exhaust will, too... again.. not much. Chip? I doubt it from all the posts I read. TB spacer? Got one... did nothing. CAI? nothing.... factory airbox with good air cleaner is more than enough.
To be honest... when you lift it with bigger tires, your best performance upgrade will be regearing the axles to match the engine RPM's back with the oversize tires. This is the NUMBER #1 upgrade I recommend after a lift and tires if you know you are done and happy with the lift and tires you choose..
~Todd~ 2004 X 4.0 5 speed---SOLD
4" Lift, 4.56's, 33" Duratracs on M/T Classics
RR SYE, Tatton CV, MML, BL, TT, Dynomax Exhaust
Hella Lighting: Driving, Fogs and H4 E-Codes
... and NEVER will be