Also a new digital source for the Blood test scene with recomposited background elements (IIRC).

And as always this is the best info we have on the TPM workflow from Knoll himself
https://www.fxguide.com/fxfeatured/art-of-stereo-conversion-2d-to-3d-2012/

There needed to be two new color timing parts to the show and Knoll used this opportunity to upgrade all the material, since when Episode I was originally finished, it was done on a per shot basis – “done sort of old style, final a shot, film out a shot, look at a print of that negative and that’s what we would final”. It went through a conventional negative cut. An optical timed IP was generated from that and then then master printing negatives were made from that timed IP. So everything audiences saw in the theater was two generations down from the original. “When the original DVD was released,” Knoll says, “it came from scanning in the timed IP because it was the simplest thing to do. But when it came time to do [the conversion], we were going to take the movie and cut it up into 2,000 separate pieces, work on them and re-assemble it, we had an opportunity to go back to the original material. We could go back to the original film-out tapes that are a couple of generations better than what had been seen. So we figured let’s do that. We made a concerted effort to collect all the bits, re-create all the dissolves and pre-wipes. So that was all pre-graded material, so we had to do all new color timing, just to have the new Blu-ray master. Then there is a device-dependent color timing that’s done to compensate for the light loss that comes from stereo.”