i have a couple of questions

What I meant by the rod torque being off a lesser amount could be factual. I doubt the torque reading on them is off by 25ft lbs like the head bolts. Its probably not a linear relationship. I bet its a lot less, considering the stock torque is 45 ft lbs, they might only be 5 lbs high, in which case I would not be concerned about it. Of course this depends on the type of problem the torque wrench has.

Bottom line is to check and recheck to make sure you are doing the right things. Dont get discouraged by this experience, It happens to everyone especially when you are starting out. Building a motor is a learning experience.