Ok, that's good. You still at 656mm?
Given the string-through holes are pre-dirilled, Mark's suggestion of longer intonation screws is a solid, non-invasive option.
There has been a history of TL kits (not all) having bridge position issues, but usually involving the bridge pickup route preventing the bridge placement for correct intonation. Generally only around 5mm or so. When you're initial report was 10-12mm, it was red flag for me, thus prompting me to off the advice above.
Now that you've worked through the points I suggested, and at least gained (or lost?) about half what you needed, the longer screws is probably your best bet.
You should only need longer screws for the E & B saddles as the rest of the strings will intonate further back then those two, but may need them for all 6.
Keep us posted!
Edit to add:
The intonation adjustment screw size are M3 x .5 x (length) - probably need 20-25mm
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