Remove the engine, trans, steering, engine wiring harness, fuse box and cluster from the 92 Auto. Put all the necessary parts from the 88 in their place. Swap fuel tanks and fuel lines all the way to the front. Leave worthless water separator on the 88. Mount the Fuel filter bracket. Drive it.
YOU might want to think about wiring in the gasser IN TANK fuel pump and running that. Nothing like a little better lift up to the pump.
This car took me a 10 days of work:

And a bit of a story behind it:
So in the last 5-6 weeks Ive been forced to get my crap running (or towed away). In that time Ive merged an 85 turbo diesel, an 85 N/a Diesel, and an 86 Turbo diesel into one mostly complete vehicle. So heres what happened.
Years ago I completely stripped down the 86 TD to a bare shell, POR-15'ed the engine compartment and installed some 02 GTI heated leather seats. And that way it sat..too many other projects and basic lazyness kept the 86TD from seeing the road.In all this time I collected parts because Im great at spending money I dont have instead of having a running VW. Enter the city of Merriam. I now have to get my crap gone, running, or running and titled or its going to get scrapped. Hows that for motivation? So both 85s were running parts cars for a total of $300. (thanks ElDrifto). I started stripping parts and throwing them at the 86.
The 85 TD gave up its suspension, fuel system, what would be a catback on a Petrol car, wheels and brakes to the 86 TD. The drive train from the 85TD went to another vehicle..well not the transmission...it got set aside as a spare. Ill come back to that in a bit. So then...the 85 N/a gave up its engine and transmission. I got it all installed with the 86 TD wiring and fired er up. Before the rest of the front end was assembled a dual downpipe and matching dual outlet exhaust manifold were fitted. In about 3 weekends time it went from a shell to a rolling, running, barely stopping vehicle.
Last weekend I was buttoning up some loose ends like BRAKES...turns out the M/c that was working fine in the 85TD crapped the bed and filled up the brake booster with DOT4. I had a new 22mm master cylinder I was saving for my passat brake swap...but I needed it now..so in it was installed. Holy crap does this car have brakes now. I also installed the exhaust system the following day. I had to fab up an intermediate pipe but that wasnt so bad.

Then I found out why the blue Jetta (that donated its engine and front fenders) was parked.

The clutch came apart and jammed a spring between the flywheel and the case...oops. It gave me a reason to install the 9-10lb flywheel.
So..with 2 decent running cars side by side..I see this only taking 2 maybe 3 weekends.