The tech trees (and policy trees) should be fixed by editing the Lua code that creates the "pipes".
I played this mod a bit to check its current state and found the following serious problems:
1. I can't select a civ from the game setup screen, I need to use advanced setup.
2. I got a Settler from an Ancient Ruins during the prehistoric era. This can unbalance the game a lot...
3. Some beliefs belong to multiple categories (Pantheon, Follower etc.), which can cause problems.
4. Many techs that are supposed to reveal resources don't do so (and these resources are visible from the start).
5. I can't see any new resources introduced in this mod on the map (although I only played the beginning of the game for now). Make sure that all resources are generated properly in AssignStartingPlots.lua.
6. The standard game speed lasts only 430 turns, which is less than in the unmodded game (500 turns). It's probably a mistake in CCTP\Various\CCTP_Game Pace Rules.sql here - I think the last line should be STANDARD as well instead of MARATHON.
Code:
SELECT 'GAMESPEED_STANDARD', 800, 60 UNION ALL -- Ancient 1000bc
SELECT 'GAMESPEED_STANDARD', 800, 75 UNION ALL -- Classical 750bc
SELECT 'GAMESPEED_STANDARD', 300, 60 UNION ALL -- Medieval 1300
SELECT 'GAMESPEED_STANDARD', 240, 25 UNION ALL -- Renassiance 1700
SELECT 'GAMESPEED_STANDARD', 120, 50 UNION ALL -- Industrial 1875
SELECT 'GAMESPEED_STANDARD', 60, 60 UNION ALL -- Modern 1987.5
SELECT 'GAMESPEED_STANDARD', 12, 100 UNION ALL -- Post Modern 2012.5
SELECT 'GAMESPEED_MARATHON', 1, 520 UNION ALL -- Future
7. I'm not able to purchase Shamans for Faith. Are there any additional conditions to do so?
8. I adopted a policy that, according to the description, gives +1 culture to the Tipi improvement. But my Tipis don't produce any culture.
9. The AI sends trade routes to me very early in the game. So it seems they get starting techs they shouldn't have in the Prehistoric Era.
10. After loading a saved game I get messages from every city state about giving me iron and not giving me iron
I also found some minor problems, like missing icons and text, bad English etc. And there are balance issues - for example it's too easy to generate very large amounts of faith.
Conclusion: the mod has lots of potential, and can become the greatest mod for Civ5, but it needs lots of work.