I'm not sure if the harnesses for the power locks or mirrors were installed at the time the car was built at the factory, but they are a plug and play once you install them. I say that, because the cheaper or not loaded versions are like that for a reason, it didn't get installed. I believe the Geo Prizm models are similar to the Corolla models as far as the electronics go, other than the dash layout and the radio (Geo's got the Delco radio, versus a Toyota radio), but both used the same speaker set ups.
At this point, you could go either way as far as swapping the engine, or converting/installing the items from the LE into the DX. I'm not sure which is quicker, as it would depend on how good you are at reading wiring diagrams, and what sort of tools you have. Swapping the engines is a very involved process too, but might be easier. You'd need a FSM (Factory Service Manual), so you can study the different items of what you want to do, then decide which are things you can do, and which are not. You can rent an engine puller (cherry picker) from the Zone or a rent all place, so you wouldn't have to actually buy it (although a few rentals and it would pay for itself), or you could borrow one from a friend. If you have a garage, you could use some of the cross support beams in it to pull from, or even use a child's swing set. I've done all of those over the years, so I have an idea of what I'm talking about (not blowing smoke up your butt). However, if you live in an apartment complex, you might need to have a friend that will let you work at their house, as most apartment places don't allow working on cars.
Personally I'd fix whichever one has the least amount of rust/body damage, but then I live in the salt belt, where rust is a nasty 4 letter word. And cars and trucks of almost any age get it. I know I've replaced a lot of rusty metal in my own Geo Prizm over the 10 years I've had it.
I hope this helps, and gives you some more info to think about.