I built a 4.0L up a while back, before I was on this site though. Here's how I did mine:
Early '90-94 (larger chamber) heads, home ported
'90 block, bored .030" over
SOHC flat top pistons, block milled so pistons were even with deck
Comp 422 cam, rockers and pushrods off a 2.9L (yes, they work fine...)
Headers
E85 fuel (105 octane)
That thing had guts. Here's some pics:
http://i231.photobucket.com/albums/ee229/acstech/HPIM0375.jpg
http://i231.photobucket.com/albums/ee229/acstech/HPIM0351.jpg
http://i231.photobucket.com/albums/ee229/acstech/HPIM0353.jpg
http://i231.photobucket.com/albums/ee229/acstech/HPIM0354.jpg
http://i231.photobucket.com/albums/ee229/acstech/HPIM0356.jpg
You can put earlier pistons on your motor to give a nice compression boost. SOHC pistons are flat top and would raise the compression even more, but it would be too much for pump gas.
I would use the earlier '90 to '94 pistons and a Comp 422 cam. That'll raise your compression a bit, but with the bigger cam you shouldn't have problems on pump gas. Then put headers on it. Porting your heads helps but don't go overboard. I polished the chambers on mine but I probably didn't need to. My machinist put bronze wall valve guides in mine, and I think that was a good decision. It put the valve stem seals lower to allow for full opening of the valve. I think the spring retainer squishes the stock valve stem seal with the larger cams.
I know I'll probably catch flack for the following, since it's not the conventional wisdom, but here goes...
Contrary to popular belief, the adjustable 2.9L rockers and pushrods will work on a 4.0L. Mine ran fine with it. The only thing is that the pushrods run real close to the intake ports, and you'll have to play with it a little when you're assembling it so everything lines up right. The other thing is that the oiling hole on those rockers has a small boss that oils the pushrod cup. The pushrod cup will run into that on a 4.0L with a Comp 422 cam. A quick and careful trip to the bench grinder fixed mine right up.
The reason for the adjustable rockers is that, IIRC, the base circle of the aftermarket 4.0L cams is smaller than the stock 4.0L cam. With the stock 4.0L non-adjustable valvetrain you may run into problems. With it being adjustable you can properly set lifter preload.
Let me know if you have any questions.