I am re-building a 1981 Jeep Scrambler with a 258 six cylinder now.
I want to go to a fuel-injected motor and am not sure where to start.
All running gear is stock and will be changed. I also need info on axles  

a late model sbc/4l60 auto or a 91 and up jeep  4.0/nv3550 and a pair of d 44's,
07 rubicon axles are very affordable from mopar. they have e-lockers, front and rear disc brakes and 4.10's out of the box for close to 3000 a pair.  

A Jeep simply is not a Jeep anymore with a SBC in it. If you want a V8, a AMC 304 or 360 will basically bolt right in as the 304 was a option until early 80's. Nothing wrong with a good 258 either and a good fresh one with some decent gears behind it can do a very fine job off road and use less fuel doing it too.  

the jeep becomes a dependable jeep with a sbc and theres no problems with cracked manifolds or finding parts with a reasonable price tag....  

I plowed snow for 15 years with a J20 that was AMC powered and I had not problems with reliability. I have owned truck for 23 years now and I can easily say that it was the most reliable truck I every had. Never failed to start and run well. BTW the reason exhaust manifolds can crack on them is because they are torques too much. The are designed to float on heads and over torquing bolts will not let them float and they will crack. Also no 350 powered vehicle I ever owned could match the lower RPM torque of a AMC 360. I am not down on Chevies but I believe a Jeep should be a Jeep and not a CHeveep or a Jevy. BTW, AMC motor parts are not hard to find and in a 360 you can use 343 pistons as all 360 ones are dished and 343 ones are not and 401 speed parts are not hard to find either and while the 304,360 and 401 share same block, unlike GM 400 SB the AMC block has different bore centers and has full water jackets in a a 401 and all AMC 360 blocks will safely bore out to a 401 bore too as one casting was used for both motors. AMC made some fine motors in their day.  

i'm a purist when it comes to brand loyalty. i believe in keepin a AMC all kenosha, a chevy a chevy, a mopar a mopar, etc.
if you can find one, build the AMC V8, if not, build the shshshsh...ugar out of the 6!