What happend was that I used the Ubisoft folder instead of the SHIII folder to extract the utility into.....
Then I went ahead and installed all the others GW...NYGM tonnage...NYGMterrain add-in plus... the Unified mod.
Guess what...the game ran in the original unmodded condition....duh.....
So....I just moved all those folders and files from the UBISoft folder over to the SHIII letting all of them rewrite. as needed ... and guess what again....it works......just fine.....or has for the last couple of hours that I have been playing single missions. I am going down the Kiel canal in a new career and all looks ok to me.
I still don't have any idea whether or not I can undo any of the mods since I installed them in such a bassackward way.....but its really not a problem now. My only concern was to finish the Academy before the mods went in and made it impossible to complete....which I did before I started installing the mods.
So then...if anything comes along that warrants a fresh install I will save the files that have the academy training completed and reinstall everything fresh and hopefully the right way next time.....
....and BTW....this Unified mod project really has to be seen to be believed...it is magnificient!