I have an early '69, bought brand new in April '69. It was a transitional year, mine has a different heel (more like a Les Paul SG) and a typical '60's neck carve. I believe late '69's had a rounder neck. and may have grown a volute. I also have a serial number for a '55 Les Paul Jr.
The screw itself seems longer, not that it's sticking out more. Did you try removing the screw completly? I have a '69 Special with a wrap tailpiece, and I am in the minority here because I like the Leo Quan Badass tailpiece with adjustable saddles. It's not period correct, but you're...
The screw on the treble side looks a heck of a lot longer than the screw on the bass side. You can unstring the guitar, take the string mount portion off the Maestro, wrap the strings around the bridge and set the intonation that way, then put it all back together.
The Maestro and lightning bolt bridge/tailpiece were standard equipment. Me, I'd leave it just the way it is, not bother filling holes or refinishing, and replace what needs to be be replaced with modern parts. As mentioned, the vintage parts market is way expensive, and, I believe, has some...
I saw one on ebay last week, similar sunburst, no pickguard and those horrible butterscotch pickup rings and pokerchip. It had the anniversary 12 fret marker. I'm glad I didn't have any tequila because "...I would have had a lot of splainin' to do...."
Really nice sunburst by the way.
The white pickup covers are replacements. The Grovers are a common mod because other replacements were not readily available (I know from experience) in the late '60's early '70's, and if there was any damage to the tuners they were the only game in town. The "poker chip' is also a replacement.