Sounds like you have a good lead on this,
With regards to your entity file questions, all the items you want to adjust are in the ship files, so take your Tech ships files, Capitals and frigates and adjust :
Things to Do Entitiy Files
Reduce Hull Regen Rates all ships (Ship files) HullPointRestoreRate ##.##
This is done close to the top of the file, look for maxhullpoints.
2. Reduce or elliminate Hull Repair Abilities all ships / Change to Shield Restore / Anti Matter restore when possible
Again, look at maxhullpoints, you can reduce these as necessary.
3. Add Hull repair ability to all factions Constructors
For constructors, you want to add the repair ability to the ability slots, make sure you have like:
ability:0 "AbilityRepairDroids" entry. You can use whatever number, 0,1,2 or 3 you want, just don't duplicate, of course and
if there are already 4 entries, then choose one you want to overwrite.
4. Verify Hull repair ability for all Ship Construction Platforms and Starbases
After making the change you can verify by loading a game up, load your mod and test.
5. Increase Build Times Ships, Tech, and Installations
Again, close to top of file is a Buildtime, right under the metal, crystal costs, add a larger number, these are in seconds, so do what feels proper, if you want 5 minutes, its 300 seconds.
6. Modify Economics to facilitate larger map and longer build times balance as necessary
When you say modify economics, do you mean, slow the rate of credits and metal, crystal to your planet?
If so, adjust the time in the planet entity for TerranHomeWorld. If you mean something like more or fewer tradeships, then adjust the number of tradeships in the Tech Trade Center entity file. If it's something else, then give me an idea of what you are doing and i can try to figure it out.
7. Reduce elliminate fighters/bombers and Trade Ship Traffic
Fighters can be added, in the squadtechbomber and squadtechfighter files, in the gameinfo folder, close to the bottom of the folder. If you are removing them, easiest way is to remove the entries in the ships that carry fighters and bombers, by removing the entries or the numbers for them in the ship files. Like the frigatetechcarrier.
8. Add New planet types and Bonus's
Best way to do this is to take Uzii's mod and change the above, instead of trying to add this to your mod. Also Distant Stars and a number of other mods, I believe the Star Trek mod also has added planets, though i could be wrong on the Star Trek one.
9. Modify Tech trees to adjust Planetary Colonization Research to allow New Planet Types.
Again, best way is to take one of the added planet mods and adjust the research files accordingly.
10. Decrease Pirate Raids balance with longer game play
Decreasing Pirate raids can be done, by carefully adjusting the pirateRaidDef entry, and the
times in the gameplay.constants file in the gameinfo folder.
11. Rename Pirates as Orions
Ok, this is a little more, not much though, Go into the PlayerPirate.entity file, change the:
raceNameStringID "IDS_PLAYERRACENAME_PIRATE" line, then go into the STRING folder (open with notepad), and do a find, look for the
playerracename line for the Pirates,
Change the ID entry and the Value entry to Orion, like this:
There you go!!