REW is free, so start there if cost is an issue.
Armed with rta software, you may be able to do better (highly subjective) than YPAO, assuming you have the requisite eq and crossover setting flexibility to tweak things.
By virtue of using multiple subs, you're probably ameliorating modal lumpiness already. Don't overlook passive means (i.e. playing with sub locations) for best effect.
Adding a miniDSP seems a bit expensive, and somewhat redundant given what you already have, unless you opt for an even more expensive Dirac equipped unit. Dirac seems a step above YPAO. FWIW, I am confident in my own ability to dial in a system as good as or better than Audyssey or YPAO, but think Dirac would be hard to match...which is just a wild guess, as I've not yet used Dirac.
Not sure about the warning in the miniDSP manual, but anytime you're doing calibration realize that test signals, particularly continuous signals, have way less crest factor than music, and are more demanding of speakers and amplification. Just don't do anything foolish, like testing the acoustic roll-off of your mains at 95db using test tones and you should be fine.