Regardless of the size of the 29 gal tank, it will fit under the 90 gal canopy. When you start cycling your new 90 gal tank it won't need a sump or a skimmer for a while, so I would continue to run your 29 gal under the 90 (or anywhere) until its time do something else.
Many use glass tanks for sumps, but this can pose some problems like 1234 said it can be too short for a long term sump. You would have to keep the water level down quite a bit.
In my experience (depending on what you will use the sump/refugium for) you have to treat the sump/refugium as a display tank as well with proper lighting if you will be throwing frags down there or they will die.
You can jerry rig a baffle using a container of sorts to deflect the water from your overflow. If you don't drill the glass you'll likely have problems priming your pump occasionally. Acrylic sumps are expensive, even more so when you go bigger.
Rubbermaid totes work well. I prefer Steralite totes - the clear ones, that would be my suggestion. It's cheap and there are a lot of benefits to using these. You can plumb through them easily. You can link multiple totes quickly/inexpensively/easily. Your options are limitless and starting from scratch is not a loss of investment.