Unless you have a big box phobia check Home Depot or Lowes. We used a Schlage brand. We found in stock 4 sets all keyed the same....there is a number on the box indicating what the key is. They said they would rekey the rest for $5.00 each. We ended up just putting the 4 keyed alike in the regularly used entries. I got a cheap keyless doorhandle for one door, but the batteries went dead pretty quickly and I haven't bothered to replaced them. Doing it over again I would get one that requires no batteries or power.

The 'bumper' can be as discreet as a little clear silicon self-adhesive dot (you can find them in any craft or hardware store near the picture-hanging supplies), or something like the rubber door-handle bumpers you see in offices. The right bumper for you would depend on your design and on how fast you normally slide the door. Do you need heavy-duty protection, or will something lightweight be sufficient? I've always heard that once glass has been tempered (and shower doors will have been tempered) that it is no longer possible to drill holes into the glass without causing it to shatter. I'm no glass expert, but a quick call to any glass shop should be able to confirm or refute this 'rumor'. I can't imagine what you could use to 'fill' the hole if you were to remove the long horizontal handle, but you may find that just leaving a hole (finger hole?) wouldn't be so bad. Another possibility would be to remove the standard handles and use decorative cabinet knobs with backplates instead. I've done this on all of our frameless shower doors using a cut-down synthetic wine cork to fill in the larger-diameter hole between the backplates. You can't see the cork once the knobs are installed back-to-back, and the design possibilities are vast.

Check the thickness of the door (where the handleset goes through the door). Also check the distance from the edge of the door to the center of the holes for the handle and the deadbolt (should be the same distance). Most handlesets I've seen in stores like HD offer some adjustability in both measurements, but the container for the new handleset should tell you what ranges of fit it offers.

The amount of viewable glass will vary by manufacturer, so that should really be a non-issue. If you are replacing the door/sidelites with the proper style, color, size (meaning total unit size) to meet HOA requirements, they really can't ask for anything more. As Mmaserl said, I'd not engage in any discussion about glass differences, etc. Just supply a work order showing the 36" door, 12 sidelites (full or half view or whatever), and the appropriate colors and style. *IF*, it is something that they brought up in the first place, I don't think it would be out of line to request a variance. A factory assembled unit will offer a substantially better finished product (appearance AND performance) than sidelites that are cobbled together by a local glass shop.