I will have to look at my old manifolds, but I don't think there is enough room to do a "Y" pipe on the drivers side, but there ,may be just enough. You would have to cut/mod the drivers side manifold so you could drop the x-over down to the drivers side. This wouldn't be too hard, but given the limited amount of room it will be tight. With a 2-3" body lift you should/would have enough clearance to run the x-over over the top of the top of the bellhousing and not have to mod the drivers side, other than welding on a block off plate. Of course this wont likely increase performance much, other removing the excess heat from the drivers manifold, and some improvement in airflow.

If you have the disposable funds for headers, the concerns listed above can all be avoided, though I would recommend a 2" body lift along with the heat shielding. I don't have a BL on my '90, and there is only 1/2" of clearance between the passenger floorboard and the header, however w/a 4x6" piece of heat shielding between the firewall and the header and there isn't a heat issue either. A starter blanket for the starter and your starter is shielded from the heat, just remember to rebuild your starter when installing headers, it is a PITA to get it out/on, and then try and cover it with the starter blanket.

I ran the x-over between the transmission and the front driveline, so there isn't any issue with the rocks on the trail.

Downey headers retain everything in the stock location, so that also isn't an issue.

I say give it ago w/one of them at least while you have them apart, it wont be very easy at all once you get the heads back on, whichever way you choose to go. If you can't find a spare 3.0 drivers exhaust manifold, or FUBAR the one you have, let me know I don't have plans to use mine.