I would start by going over to http://hptuners.com/forum/ and http://ls1tech.com/forums/forumdisplay.php?f=7 and looking through their PCM tuning section. They both have good writeups on where to begin.
I would start by removing as much TM as you feel comfortable with. Then move on to the VE tuning. After that, you can work on timing and WOT settings.
But read up on the stickies they have. Thats were I've gotten most of my knowledge from.
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