Okay here is what I would do. If you want to be able to use both motors. Order the 331 stroker kit in a 28oz imbalance. Purchase a 28oz balancer and 164 tooth flexplate that will work on both motors and be able to use the same tranny. Rebuild the stock 69 first and get it installed then build the 331 85 block after that. This way you are never without a good motor in the car. What you have right now is 50oz imbalance which will be useless when your done with both builds. you will be fine but if it were me I would buy two 28oz balancers cause they are a pain to change from motor to motor.

______________________________________
69 Mustang 331cu in DSS level 20
TFS track heat, DSS rockers, lift:.573 .276, Bigs 750, MSD 6AL & billet dizzy, B&M 174 @7psi, AOD 3.5k stall, 9" 4.11