which bellhousing are you currently using on your small block? If your using the lakewood, your fine.. if your running the stock G body 606 bellhousing, you'll either have to find a 153 tooth flywheel, or upgrade to the lakewood bell.
I've been following your buildup too as my malibu is a factory 4 speed car and i'm looking into the 5 speed TKO, but i'm also swapping in a big block at the same time, and swapping in a 9" rear end first. Did you actually need to cut that big of a hole in the side of the factory 4 speed hump? That's the only part of the swap that's bugging me!..
I think your vibration is either driveshaft, or rear end related.. have you considered measuring the factory angle etc. on a "stock" malibu or G body at the rear of the transmission, and the rear end, and comparing them with yours? My malibu would vibrate at 80 to 100, but over 100, it would clear up, then come back around 130ish with 3.73 gears, I replaced all bearings etc, in the rear end, and it cleared up. I only did that because I knew everything else was "stock location" and hadn't been changed.