Hi KAD and welcome to the forum!
That's an interesting example of a T-100D. Here's some info and answers to your questions.
-- The inlays are definitely not standard. I think I may have seen these on Guild acoustics before, but I'm not an expert enough to claim that they signify a custom order.
-- The truss rod cover is almost assuredly not stock.
-- The Grover Rotomatic tuners became standard on some models in 1965, so they're probably original.
-- The switch tips on these are usually metal with a domed top rather than a completely round top.
-- The pickups are single coils known as "mickey mouse" pickups because the surrounds are usually black, and the tops white. Yours are different in that the outer rim of the pickup is white, whereas they're usually chrome and come up over the edges. This isn't so unusual, though, and other examples like yours pop up occasionally.
-- The bridge is an oddball. These bridges were standard equipment on the solid body S-series and M-75s, and rarely appear on the semi-hollow Starfires. I've never seen one mounted on a wooden base before, so I don't know if this was a factory thing or something someone else added later.
-- The attempted replacement pickguard is facing the wrong way, which you know, of course, and the logo is more associated with 70s-era Guilds. Guild recently started offering replacement pickguards, however, they don't offer one for your pickup configuration. That doesn't mean that one won't work, but the routs are probably going to be too big. By 1965, the stairstep style was more common on T-100s, and since the super structure is the same, the closest match might be the Starfire. You might want to email them to see if they have any without pickup routs, since the SFIII are routed for the mini-humbuckers and will be too big.
-- Is the label legible inside the guitar, and what does it say?
For replacement parts, I would first try Guild super expert and LTG member
Hans Moust. He might be able to help you with some vintage parts and most definitely with learning more about the history of your guitar. Guild put out a lot of guitars that stray from the standard model appointments in the catalogs, and it's always fun and interesting to see them.
Cheers!
JP