Elaine I think you made a good choice. I would suggest a cannister filter.
Your 2x4 roof rafters will certainly hold an air filtration unit. Rather than attaching directly to rafters, I would surface mount a couple 2x4's with lag bolts. This way you can place the unit much more easily.
In a shop your size, the filtration unit does not need to be much. You may even want to consider building one. There are many DIY videos on YouTube.