Jesse: I know you tried a few different pups in your RGT, was it the CL/LF set that you settled on?? Did you have any quack type problems??
I honestly should have given the stock pickups more of a run so that I would have had a better baseline. I got the guitar with the original strings on it, so I should have at least changed the strings before deciding that I hated the pickups.
You're correct that I went to a Crunch Lab/Liquifire setup. I did not like the Crunch Lab, nor did I really care for the D Sonic I had in a different guitar. I just don't like pickups with the highs rolled off like that and I also think I'm done with super high power pickups. The CL may work for John Petrucci's particular setup, but that isn't a setup I care for or want to duplicate.
What I have in there now is an Evo 2. I would say that the RGT is still not my favorite sound out of my guitars, but I think the Evo 2 solved a lot of the issues I had with the sound. The highs could be a tad warmer, but at least they're there.
The Liquifire in the neck is a complete revelation. I can't say enough good about this pickup. It gives an almost perfect blues tone in the RGT. For me I always feel like neck pickups rarely give me a sound I want to use, but this is an exception. The RGT has become my preferred guitar for blues. I like practicing to blues backing tracks because the slower tempo gives you a good opportunity to experiment a lot without having to worry about keeping up with the beat.
So yeah, I'm happy with the Evo 2/Liquifire combo in the RGT. But everyone likes a different sound and you may not like what I like. I'd say that I see you generally recommending pickups with fairly similar EQ curves (Gravity Storm, Breed, F2, etc) and I'm usually going in a different direction (PAF Pro, FRED, Evo 2) where the bass is rolled off.
Just yesterday I was playing my RG8670 which I installed a Norton in. I was trying to convince myself that I like it and I shouldn't install the FRED that I just got in. I had almost done that when I played something I've played on other guitars and it just sounded wrong. The bass was just drowning everything out (mahogany guitar probably doesn't help). So I put the guitar down, plugged in my FP with PAF Pros and instantly got what I was looking for.
So yeah, super long reply but my point is figure out the sound you like and then try to figure out why a particular guitar may not be giving you what you expect.