Mark... I agonized in my mind what I would do if confronted with this problem, and admit that's a tough call. At the end of the day it probably comes down to what you can "live with". I agree with what other guys have said about all pices having their "issues", but again, it's what you can accept. It sounds like you went through a similar process and came to a conclusion. Good for you. I think in the end, you'd be agonizing about an off center ram rod hole, which might effect the build going forward, and also bother you. While difficult, I think you made the right decision for you going forward with the project. Look forward to seeing some photos when it's finished!
Ed