Ok. Here's a walkthrough for making a custom GaussBlast ability and adding it to 1 capital ship (we'll add it to the vasari's capital battleship "CAPITALSHIP_PHASEBATTLESHIP.entity")
Go ahead and actually make this with me so you can make sure you've got it down:
1.) Make a new folder anywhere named "TestMod" Within this, make 2 new folders called "GameInfo" and "String" Verify you use the same case as I type, the game doesn't seem to make a distinction in all cases, but if you scrutinize for case, you might catch any typoes.
2.) Get a hold of STRing versions of the following ent1.01 (or whatever version you're making this for) files and copy them to where I specify:
2a.)"AbilityGaussBlast.entity", "BuffGaussBlast.entity", and "CAPITALSHIP_TECHBATTLESHIP.entity" to "TestMod\GameInfo"
2ab.)rename the ability and buff files now by adding a "2" to the end of both (before the ".entity" of course)
2b.)"English.str" to "TestMod\String"
2c.)"entity.manifest" to "TestMod"
2cb.)open "entity.manifest" now and add the following two lines to the beginning of it and increase count by 2:
entityName "AbilityGaussBlast2.entity"
entityName "BuffGaussBlast2.entity" Make sure you don't accidentally add any empty newlines
3.) Open "AbilityGaussblast2.entity", and make the following changes:
3a.)buffType "BuffGaussBlast" ----> buffType "BuffGaussBlast2"
nameStringID "IDS_ABILITY_GAUSSBLAST_NAME" --> nameStringID "IDS_ABILITY_GAUSSBLAST2_NAME"
descStringID "IDS_ABILITY_GAUSSBLAST_DESCRIPTION" --> descStringID "IDS_ABILITY_GAUSSBLAST2_DESCRIPTION"
Save and close the file
4.) no change is necessary for "BuffGaussBlast2.entity". Don't edit it to increase power until you've successfully loaded this test mod
5.) Open your English.str file and go to the bottom. Put your cursor in the blank newline at the bottom, and paste this:
StringInfo
ID "IDS_ABILITY_GAUSSBLAST2_NAME"
Value "Potentially Uber Gauss Rail Gun"
StringInfo
ID "IDS_ABILITY_GAUSSBLAST2_DESCRIPTION"
Value "This is a custom gauss ability. It will be really powerful later"
make sure to hit enter after you paste so the file will have that extra empty newline again. Also, increase the count at the top of the file by 2. For some reason the forum won't accept {tab}s, so after pasting the above two lines, delete the space before the two "ID"s and "Value"s, and then hit tab for each one (4 total) .Save and close this file
6.) Open "CAPITALSHIP_TECHBATTLESHIP.entity", and make the following changes:
ability:4 "" ---> ability:4 "AbilityDisruptiveStrikes" (you're moving this here cuz it's passive and doesn't need clicked)
ability:2 "" ---> ability:2 "AbilityGaussBlast2" (this adds the ability to the ship and makes sure it's in a spot where you can actually click it once "purchased" for you capital ship)
save and close the file
7.) Copy (or move) your "TestMod" folder to your {ModPath} folder
8.) fire up the game; unselect all mods; select this one; start a new game as vasari; create this ship; verify it works correctly (one thing you might notice is that the text wrap doesn't seem to work for custom abilities, so if you have a long description/name for your ability, it might trail out of the ability "infocard" before wrapping. If I had to guess, I'd say we need to make our own custom infocards to contain it correctly, but it doesn't bother me enough to mess with that 
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That's it. If you followed these instructions to the letter, I'll guarantee it works (I did each of these steps as I wrote them, and it worked perfectly -except for the wordwrap of course- ingame)
The next step is like Teal said in your other post: Introduce changes to your mod 1 or 2 at a time and test them ingame. This way as soon as the game fails to load/work right, you have only 1 or 2 things to focus on troubleshooting instead of the whole darn mod.
Let me know of any more questions/issues you might have!
