An 87 5-speed is shorter than the A4LD. 88 started the long manual transmissions. The cross-member ears will need to be relocated, the good news is that the holes are already there. You just have to grind the rivets out and bolt the ears up in the rear set of holes.
Side note, the front hole for the rear set is the same as the bottom rear for the forward set.
I spent a few years at car shows and on Amazon and ebay rounding up factory wiring manuals and then I sat down and spent a month tracing wires, tracing diagrams, and building harnesses. Then I had a few gremlins to track down once I got it all installed.
Every swap is different, different donors, different recipients, different options. It is usually the wiring that is the worst.
Your 87 has a dual pump fuel system, but it will provide enough flow and pressure for a 4.0. It is actually capable of more than you need.
Be ware of the wiring. The EDIS module is not part of the harness, it is a separate piece that plugs into the harness, and the plug and most of the wiring for it is part of the headlight sub-harness. The headlight harness has to be changed, but the plugs on it are wrong for your bulbs, so the plugs need changed out.
It just one of those things, people can steer you in the right direction, help you figure out the broad strokes of what needs to be done, but you kind of have to figure out the details for yourself.
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