So I found a post in the 2.70 patch notes by Old-Spider (reply#6), that talked about how his mods weren't showing up in game and found out that it was due to his naming convention of his mod folders. He used a period in his name, (i.e. "2.61") to show that they were updated to the latest patch. When he removed the period from the folder name, his mods started to work in the game. I had also done a similar naming convention (ALS_Star Trek_2018_Crusade 2.71). So I removed the period, and still no luck.
Then I remembered I had changed one other name in the mod and wondered if that might have the same issue. I had in my troubleshooting renamed ShipHullStatDefs.xml to Allen_ShipHullStatDefs.xml. When I changed the back to it's default name,,,,,,,,
POOF IT WORKED.
So out of this,,,,
1. Names of mod folders DO NOT like periods.
2. Names of Default .XML files in a mod folder are not read by the game if they changed from their default name.
So hopefully this helps others, with similar issues.