I am trying to create a patch for one of my mods i have been working on and NOM, but every time i run the construction set i get alot of errors, then the construction set crashes.

here are the errors i am getting:

Chunk size 10 too big in chunk WEAT_ID in form REGN_ID.Max size is 8, data truncated to "#".Unknown SSCR_ID in ConstructObject.Unknown SSCR_ID in ConstructObject.Unknown SSCR_ID in ConstructObject.DataHandler: unrecognized formLook in the Warnings.txt file for more info.Chunk size 10 too big in chunk WEAT_ID in form REGN_ID.Max size is 8, data truncated to "".Region 'Felsaad Coast Region' Weather Chances do not total 100 percent.Chunk size 10 too big in chunk WEAT_ID in form REGN_ID.Max size is 8, data truncated to "".Region 'Moesring Mountains Region' Weather Chances do not total 100 percent.Chunk size 10 too big in chunk WEAT_ID in form REGN_ID.Max size is 8, data truncated to "".Region 'Isinfier Plains Region' Weather Chances do not total 100 percent.Chunk size 10 too big in chunk WEAT_ID in form REGN_ID.Max size is 8, data truncated to "(".Chunk size 10 too big in chunk WEAT_ID in form REGN_ID.Max size is 8, data truncated to "#".Chunk size 10 too big in chunk WEAT_ID in form REGN_ID.Max size is 8, data truncated to "#".Unknown SSCR_ID in ConstructObject.DataHandler: unrecognized form

Those look like the same errors that occur when you've installed the expansion in the wrong order.
It needs to be MW->Trib->BM
No need to uninstall anything, just reinstall Bloodmoon.

You don't get these errors when you play? Just in the CS?

that is correct, and i have installed the expansions in that order. None of these errors show up in game. I am using the code patch aswell

You can install in good order, but something happens with Bloodmoon every so often. Reinstalling the Bloodmoon alone should fix it, try.