Pit calculator will get you what you need for correct stack. 2.5" is too small for smoke stack. I would have to said 4" would be the minimum in my opinion. If everything else measures out correct than stack should be easy fix.
I also agree with what Rodcrafter said... "That baby will work great when drafting right". I've built 4 rf smokers in the last 2 years that have all worked so perfectly. Having 100% success with the pit calculator I am always surprised when someone wants to deviate from its calculations or read posts like yours that have clearly large differences in the dimensions.
Run your numbers and use that as total confidence to make the changes it suggests. It's all about fire management and that becomes easy to do when your equipment is dialed in properly. If you think I knew what I was doing when I'd started, it only LOOKED like it. The expertise was right here.
Make no mistake, there ain't no powder in this Puff ! And... I'm not really a crazy person but I play one in real life