I added completely new block, called QuarryPlus, with quarryplus:quarry as registry name. I didn't replace the old one, with quarryplus:quarryplus as registry name, to avoid bugs from NBT incompatibility. These 2 have the same textures so you can distinguish them by names.

The new one has GUI you can open just by right click. Old one doesn't.
Did your new quarry show GUI?

It shows the GUI but like, the modules themselves don’t work in the new block, like the quarry doesn’t pump fluids, the replacer module doesn’t replace blocks, and the XP module doesn’t work

Like you can insert the modules but the modules don’t actually do anything, and this is with just the quarry plus mod itself installed and Mekanism

I took a mistake on checking the module is disabled in config.
Change the config, DisableXXXModule to true and try again.

I'll release fixed version.

You can get fluid from new quarry just placing tank next to the quarry.

Config issue is fixed in v12.2.1 and extracting with pipe is implemented in v12.2.2