From my experience the procedure is basically always the same.
Remove the handle. Fill hole (weld a small patch in or put a copper plate behind the hole and then just weld the hole shut - remove copper). Now smooth out the welds. Add your favorite body filler, prime, paint. Before you do any of this - make sure you understand how the mechanism works. In fact I would install the release mechanism first (depends on how brave you are

).
You'll need to order a shaved handle kit from AutoLoc (or other brand) or talk to a local alarm dealer (best idea) about getting solenoids, switches and relays (and possibly a 'popper').
Make sure you put a mechanical release in on one of your doors just in case your electrical system goes TU.
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- Ryan