Your trans should be the correct configuration. Seems like the change was actually in the late 90s.
Not sure on the manifolds. I think the factory (truck style which is what I've got) will work, but I didn't have the engine sitting exactly where I wanted to say for sure. Not sure what other options there are. Personally, I don't want headers, so I'd be looking for a different factory manifold. I'd guess there are some tight fitting header options though.
I'm actually moving backwards on my swap... I had the sub-frame out at one time, but a couple of years ago I had to put it back in so I could move the van from my Dad's shop into my own. Right now my 5.3L and trans are sitting on the shop floor with an engine-less van parked next to it.
Here is the last activity on my van... Sad for sure... Just too many other projects and a shop that is a true disaster area to work in. I'm trying to get organized though!
http://astrosafarivans.org/bb2/viewtopic.php?f=2&t=9371
It does look like I tried to drop the engine back after reversing the LS mounts and I still have pan clearance issues. I can solve my pan clearance issues by raising the engine up since I'll have 5" of body lift to work with, but I was hoping to keep this part all bolt-in. (This might also solve manifold issues. Raising the engine up does offer up more pan ground clearance which is a good thing!)
You asked about moving the engine/trans back... with the body lift, you may get a bit of room, but I think where the doghouse meets the floor is going to limit you.