Tanks function best with a vacuum, it tends to be what keeps them from leaking. That can be hard to do with a different sized tank, but I guess if it's not too crazy a size difference you could try it.
I would most definitely a) order replacement glass that fits and b) try filling it OFF your mod. You have a better than average chance of a huge puddle when you try to fill, so do any and all experiments like, well I would do it over the sink, probably.
Good luck,
Anna