Ok boys, note to selves...
I wish I caught this earlier. The trans I picked up apparently came out of a '91 CRX Si, but I found today that it won't work for my setup. Either the seller lied, or he was not the original owner and had no idea the trans was not original. The trans has a 21 spline input shaft, which only came on '88 Civic's and CRX's. 89-91 trans have a 20 spline input shaft. My stage 2 clutch won't fit this spline and is practically new, so I'm not willing to get a new one. I'm just going to have mine rebuilt.
So, if you're looking to replace your trans remember to check for this. It's an easy thing to overlook, so be vigilant. Don't forget to look for cracks in the housing, like at the fill and drain plugs.