01 Build lotsa goodies, questions

Hi everyone I'm building my 1st XJ and it's very cool. I've done a few CJs, a TJ, ZJ, WJ, and a few F350s.
2 very experienced friends of mine are doing most of the work as I'm out of commision for a while after some recent surgery but here's the build;

2001 4dr
newer 4.5L stroker engine(1993 YJ 4.0L HO block (125K miles on it, zero cylinder run out), pistons, head, stock cam for now
-1976 258/4.2L crank/rods (54K miles)
-new cap, rotor, plugs, wires
-all new gaskets and seals throughout
-new main and connecting rod bearings
-crankshaft spacer for the serpentine harmonic balancer
-new water pump (Advance Auto)
-new piston rings
-honed cylinders
-painted really fast lime green)

5.5" lift, gonna be all spring lift
33" AT BFG, I might do some 35" TRXUS or MTZs
Arb bumper(coming up from NJ) hopefully,
Warn 9500 winch
8.8 rear 4.10s w/locker
HP30 4.10s w/ LS front
Longarming the front
Sliders tied into unibody stiffeners
full roof safari rack
a couple Hella front lights
Skids? What should we protect and what's good?

I got a few questins for you guys, search didn't help much;
Can I use a old style header (91-98) on it? Is the connector between the s-pipe the only difference? Will the newer intake interfer? I know the newer exhaust manifolds are 2 piece and a real PIA!!!We're doing the whole exhaust at 2.5" Mandral bent.
Do I need a adj MAP sensor and 24lb injectors? The 4.5 came out of a YJ and ripped pretty hard in it. In this XJ with 3.55s and 33s it spins them at 40mph already!
I'll be adding a 62mm TB, spacer and big stupid cone intake filter.
Can 5.5" lift clear 35s with some aftermarket flares?

Do the 01s come with electric fans already or should I add it?


Thank you
Paul

"01's have elec aux fan and mechanical primary fan. Read about Taurus fans. You can use the older exhaust with a newer intake. Possibly a little grinding (not much).

I've done a lot of engine block inspection. For my educations, could you please explain "zero cylinder runout"?

have you driven the yj with that engine in?

35s need lots of trimming and bump stopping with 5.5" lift

My friend working on drove it last night, spun those narrow 33s easily w/ stock 3.55s. I have no reason to ever doubt his word. I'm actually not quite sure what the zero runout means. I didn't want to leave it out of the desciption. And no I'm not an idiot, I know what everything else is, lol.

We have some extended TJ flares that we're gonna fit after some trimming, I might stay w/ 33s, I can't see a huge advantage by going to 35s.

35s get your axle up higher so you dont high center as easy

Without going higher than the 5.5" we already have it is tough even w/ trimming I think. Honestly this is mostly road driving, maybe 5% offroad and on sundays it will be one of the family vehicles especially for our little adventures in New England. The 1 inch of clearence is nice I know. My 99 superduty has 38s and 4" lift and I slide right under the differential as do many logs and rocks

ive seen people stuff 37s under 2" lift. i know a few guys that are running 35s with 3.5"

Id say zero run out is a leak-down test, but just a guess.