If you're doing an engine swap "properly" then you probably want to:
Rip out the engine, engine loom etc
Swap out the fuel pump for an uprated item; Walbro 255lph is a popular choice although depending on target power you might have to go bigger
Fabricate your engine mounts, fabricate adapter plate to your desired gearbox and/or swap gearbox and fabricate the mounts
Drop the engine in
Drop in a new ECU with wiring loom, figure out how to 'piggyback' the relevant signals into/out of the original ECU to drive the clocks etc
Enjoy
Sounds so simple, doesn't it

Once upon a time it was a lot easier - no electronic clocks to worry about, no ABS, no TC etc.. All of these things are driven from or feed signals to the ECU now, however, and the hard part is making sure you can make your aftermarket ECU talk the right way to all the ancillaries, assuming you want to keep them.
The actual swap & fab work is still the same as it was 20 years ago, so that's pretty well understood
