The T-100 guitar is probably my favorite guitar of all time! I've owned a couple (and foolishly sold them), and I'm still in the process of totally rebuilding one that was found in a trash can. I agree with just about everything that has been recommended or suggested for your T-100D, so far. I checked Hans' book, too, and it looks like your serial number places it in the transition period for pickups - if it was built in 1965, it might have had the larger (think P-90) style single-coil pickup, and if it was a '66, it likely would have the "Mickey Mouse" single coils as previously stated. As far as what sort of work you want to do on it, there's a few options.
Since your uncle removed a bit of the top (and probably a bit of the bracing) to fit in the humbuckers, you really aren't going to be able to do a full-on restoration to bring it back to original specs. But I get the sense that you want to get it as close as possible in terms of sound, as well as getting it close to original condition. Here are a few possibilities:
1 - Just get it set up and play it as it is. Depending on the quality of the humbucker, you might have a great-sounding guitar just as it is. Try not to change anything else unless it is a change that brings it back to original specs (e.g., if it has the original wiring harness, don't change it out unless it is totally shoy - clean it up and keep it in the guitar).
2 - Remove the humbuckers and replace them with some sort of single-coil pickup. I would recommend taking a look at Pete Biltoft's pickups at Vintage Vibe Guitars
http://www.vintagevibeguitars.com/ . Pete has some humbucker-size single coils and he can also make a custom pickup for you, too.
3 - Try to bring the guitar back to original as best possible by removing the pickups, replacing the wood grafts with the appropriate type of wood (maple) and trying to get stain match, routing to specs and replacing the humbuckers with the correct pickups for this guitar. This would certainly be the most expensive option unless you did most of the work yourself. If you choose to get original pickups, be prepared to spend some $$$! Same goes for pickguards, bridges, harnesses, etc. - trust me, they are hard to find!
Opinion-wise, I think that options 1 & 2 might be the most cost effective. I think I would try to get some single-coil pickups for the guitar, since that's what was used at the time it was manufactured. Regardless of what you do with it, it will still be one of the best-feeling guitars you could possibly own! The weight, balance, resonance, and sound from the T-100 is just plain wonderful. You indicate that the guitar was inherited from your uncle - if he has passed, there would be no better tribute to him than playing that guitar every day in his memory. If he is still alive, just remember to still play it every day, but make sure you give him a big hug every time you see him!
Have fun with it!
Dean
