teal my suggestion is to ONLY have the files that are altered for each minimod leaving all others out, that should also help with the stacking issue, as entrenchment seems to look at the first mod for a file if not found then looks in the second, then looks in the third if not found and so on through the stack until it has only entrenchment and sins left, and I think that each minimod will want it's own manifest.entity
harpo
Harpo,
Your suggestion worked like a charm!!
I was able to get the mini's to load and to play, there is some slight problems of course if i edit a file in one mini and then re-edit the same file for a different effect in a second. That means i can load and run them with others that dont edit those files, but i cant use them together. Well... i can use one of them, which ever i load first is the one that takes precedence. Anyway, thank you very much for the suggestions and the help, i was ready to throw in the towel on it, but persisted and your help payed off with getting the mini's to work. 
I will have to name a planet after you. 
-Teal