The term "shoegaze" encompasses a lot of different bands with pretty different sounds. The first band that comes to mind is MBV and Debbie's tone, to my ears, has always been pretty clean. The same goes for Slowdive, Ride and most of the other bands that one first thinks of. Will Heggie (Cocteau Twins) relied pretty heavily on chorus for his sound (but who didn't in the early 80's?).
With all the loud, fuzzy, swirling guitars, you're gonna want to sit nicely in the mix. You can do that running a bunch of pedals, but as you are noticing with your MXR, some pedals just erase you from the mix. For dirt, you might want to use an overdrive instead of a fuzz. I've had much better luck with overdrives than with fuzzes. You can blend in your clean tone with a fuzz, but you can also end up with that bass with bees buzzing around it sound. I love my VT Bass for overdrive (well, I love it for clean tones too, but that's a different story) - nice "tube-ish" sound without shelling out thousands of $$$ on a tube amp.
Anyway, I'd keep your pedal rig simple - overdrive, some kind of subtle modulation (chorus, phase, flange), and maybe a digital delay (tap tempo is nice for holding down the rhythm). I play this kind of music and I often have to remind myself that it's the guitarist's job to go pedal-crazy and my job to hold everything down.