If you have difficulties in distingushing colors, there are some mods made by RogerWong

http://www.subsim.com/phpBB/viewtopic.php?t=33574
http://www.subsim.com/phpBB/viewtopic.php?t=33333
http://www.subsim.com/phpBB/viewtopic.php?t=33411

And If you are advanced enough:

http://www.delraydepot.com/tt/sh3.htm#colorinspector

I do not know if the stealth meter could be modded to appear with other colors / shades

http://u-boot.realsimulation.com/ this is the best site to find every available mod. Also did you update your stock game with the official patch???

Play until you are comfortable with the way things work then either add some mods that interest you or ask others what they use. I myself have over 20 seperate mods loaded and love my sim.

Welcome to the new addiction friend.

The color mods I think will help a tiny bit.

Does anyone know where the stealth meter graphic file is located?

Can SH3 Commander be used with RUB or IUB?

I decided I wanted to go for a bit more realism in terms of how convoys and such work, not to mention the ranks system but when I tried to mix SH3 Cmdr and RuB it died on me as I was loading up my first patrol.

Yes it can, and I've never seen them do anything other than play well together. You might try rolling back the SH3 Commander changes, then try starting SH3 with it again.