Reformat GWX issues

[SpecWarrior]

I'm having a problem right now. I had to reformat my windows drive. I previously saved both SH3Commander and my Ubisoft files to my D drive as I want to still continue my saved games. Was running GWX 3.0. I've reinstalled SH3 to a new directory as well (I understand window may have written some files it needs to the C drive upon install, so to insure they are there, I've done the new install and have both old and new files) I've also saved the SH3 folder from the pre-format "my documents" and have moved that back over there. I have kept everything (including commander which I DID NOT re-install post-format) on the D drive.

When I install I have:
1) installed stock SH3 first.
2) then patched using "silent_hunter_3_dvd_1.4b_us" (as I'm running a disk).
3) installed GWX 3.0.
4) drag and drop "GWX_21.1_Cfg_4_SH3Cmdr3.0.7z" into SH3Commander's cfg file.

Now that you have some background I'll go over my problem. It seems the graffix look fine if no mods are installed using GSGME. But if i even roll back and install the 16km distance and English grid ref's mods I have graffix glitches in the forms of:
1)Ocean is a black void.
2)Dials missing handles, etc.
3)Helm officer present has no head (literally).

Now I have questions about installing the config files into SH Commander that I've downloaded from the GWX site. (Can't remember how I did this the first time ). 1)Do I just drag and drop the lone file into commander's cfg file?
2)Can (and Should) I just scrap everything but the SH3 folder in "My Documents" and just start from scratch?

Anyone else experience this? I need some informed help pls.

SpecWarrior