some bondo,a sanding block and some time,its no too hard,fill the hole with bondo and sand it down,fill some more,sand it down,basically keep doin this until it looks how you want it,prime it,and paint it
the rear handles off a 4 door will work just fine for you, direct swap. make sure you get a push button lock system so you can lock/unlock and get stuck out of your car when the eventually stop working. good luck.
Shaving a door handle is a big job. First you have to get the old handle out. After that you are gonna have to tac some new metal in the opening. Body filler is meant to be applied in as thin a layer as you can manage. Grabbing a fist full of it and jaming it in the hole is gonna end poorly...
After that you need to install the actuators that pop the doors open and that is a whole tech article I'm not gonna write. You can find some good video if you search the web.
I am not a pro, but I have done a lot of body work on my Teg. Here is my suggestion:
As for shaving your keyhole off the plastic handle that might not be too bad. Myself I would remove the lock cylinder and add a little bit of that wire mesh to the back to make a seat for the body filler/fiber glass. You will need to re paint the handle when you are done. After that you will need some some sort of keyless entry system.
I advise not shaving off the keyhole to the trunk. The day your battery goes dead and you need to unlock the car could be a little ugly. Worst comes to worst you can always monkey your way in through the hatch...
Yup rear handles are a direct swap. Thought about doing it to the teg after I saw an EK with rear handles, but I tend to lock myself out in sub freezing temperatures at early hours in the morning. I don't need another variable in that equation.