A crate engine is about $6800, the wiring harnes and ECU to run it is about $1900 and change. Add tax, your over $9k. I'll be looking for a wrecked 2011 5.0 in the next year or two, for my early bronco powerplant.
The wiring is not hard at all. The explorer 5.0's run off a 42 pin plug, which everything goes through. You only need about 5 wires of that plug for the motor to run. Add a couple more for oil pressure and water temp, add 3 more for OBD2 port. Splicing these wires into a couple of plugs off the original motor in your 88, and you will have a simple harness with no major wiring. Fuel lines should be plug and play, as they are long enough to reach from the trucks lines to the engine's lines. You can reuse the stock exhaust manifolds till you decide to upgrade to headers.
Going carb you will have to change out the intake manifold, rewire the fuel pump relay, install a fuel pressure regulator, as well as still wire up your oil pressure and water temp to the trucks harness. Unless you already have the intake and carb, they can be extra $$ not set aside for the build. I have done both, efi and carb to efi vehicle swaps, and I prefer staying with efi. To me, its much easier. I'd be happy to help you with the wiring if you need it...
SVT