From what I have read 35-37's with a 4.0L you don't have to go one ton axles. 35's are usually ok, 37 seems to be when you start having issues.
You didn't mention any kind of budget, with unlimited budget call up dynatrak or currie and have some killer axles made.
JK axles would be great. For a TJ (I know you said YJ) I think TJ Rubicon axles are great, you can find them usually as a set for $3000-$5000 which for a tj is not really that bad for a set of drop in upgraded locked axles.
If you want to keep the budget reasonable and keep the width I think it is pretty hard to go with anything other than a ford 8.8 out of an explorer for the rear. It is basically a small 1/2 ton truck rear end, as strong or stronger than a d44 and they can be found in junk yards with disk breaks. 8.8's were used in trucks, broncos, and mustangs so gears and lockers are plentiful. If you are going with an 8 lug nut axle it is tough to beat the gm 14 bolt.
As for the front, there are not too many options. If you are going with the 8.8 in the rear, your most likely option for the front is to upgrade the d-30 up front. If you are going 8 lug full size d44's can be found for pretty cheap. But if you are going to be narrowing it I would say skip the d44 and go for a d60. d60's have come down in price, I have seen them sell on this site for as low as $900.00 complete (years ago they were going for $1400.00 complete) I have also seen a couple d60's from 86-ish-97-ish ford trucks in junk yards. (not the ideal d60 but can be a good axle depending on what you are doing)
also converting a yj from a driver side front diff to a passenger side may be worth looking into. a dana 300 t-case can be swaped in, depending on the tcase that is in there it could be made into a doubler with a dana 300 so then you could run the passenger side front axle. If you are keeping leaf springs it is not like you have a track bar to deal with. The body might be in the way, so install a short body lift or clock the t-case down.
ok now that I have said that, google around with all that info to see what you can find.
nathan
99 xj 4.0l, ax15, np231/d300, d60 lockrite, gm 14 bolt detroit, 37 old mtr's coils and links all around
build thread
http://www.rme4x4.com/showthread.php?83436-Nathan-and-Tanja-s-99-XJ-Build-up