Congratulations!
Many of us like the VP/60’s bridge and tailpiece. I’d be hesitant to change it.
It has been a long time since anyone mentioned intonation issues with one. And that was usually with the E string if heavier gauge strings were used. Your D saddle looks to be way back from the normal position. Is that your main issue? That bridge shouldn’t be an issue with standard 45-105 strings.
I would loosen all the strings and make sure there is no string twisting going on. And make sure there is no binding at the nut. If there is, a little graphite in the slots could help. Try that first. Then reset the saddles so they look like this:
View attachment 5234201
Then adjust the intonation of each string from there.
Once dialed in, you’ll love the Thunderbird.