If you're running 2×9 you would want the BB a touch longer, if anything because you will be using the 34 ring all the time on the smaller cogs and the granny mainly on the bigger ones.
When I transferred my chainset from a Cannondale hardtail to my Cotic Soul (using a 2 ring set-up on sq taper, 68mm shell, just like you) I initially used a 107mm BB but under pressure the r/h crank tapped the chainstay (big tyre clearance on a Soul). I tried a 110mm but wierdly the whole extra 3mm seemed to be on the l/h end. When I went to a 113mm, it was all fine so I left it.
I find that my max out-of-the-saddle effort is usually in the 34 ring and one of the middle sprockets. 34:18 or so. That's when I really want my chainline to be straight, which it is with a 113mm BB.