Well.....good luck with it, Crawdaddy. You'd still have to put the bike on a Dyno to know for certain what your AFR is doing. I simply can't say whether the FMF unit is adequate with the 290 bore. I never tested that combination, as I ordered the Power Commander parts together with my Athena kit.
Myself, I'd probably lose sleep over it. I hate speculating over issues that can be measured precisely. If you study my dyno runs (charts posted at WRRdualsport.com) you can observe the AFR when the 250cc bore was running with the FMF unit. It was running a bit lean in the lower rpm range.....from idle to about 3,000 (if I recall correctly). Thus, the dreaded snatchy take-off. So, that would be a particular area of concern for me.....switching to the 290 bore, as the FMF provides no adjustments for that part of the curve. Zippo!
Go find a Dyno.