:-( Dang, you've already tried what I was going to suggest; dropping custom textures and so on.
I believe that there is a configuration file somewhere that tells MUI what to load at boot. You could try renaming that file to force MUI to launch without loading anything custom that you forgot to remove.
Also, IIRC, if you highlight the MUI icon and select Info from the menu, you'll have the opportunity to adjust MUI's stack size directly. Mind you, it's possible to set it too low, which would prevent some programs from working correctly.
Voyager has it's own stack size too, but again you'll want to be carefull when tweaking it.
;-) Another approach would be to add more Chip RAM, if you haven't already. For most models of Amigas, it's possible to expand the Chip RAM to two megabytes, instead of the lower sizes that came as standard. This requires an extra bit of hardware.
At the end of the day, though, you'll only have six megabytes of RAM at best, and some graphically intensive web sites will require more just to open their front pages. So, you'll always have some site that won't work.