Definitely sounds like the problem has to do with the booster. I know the booster is new, but.... since you replaced the MC twice I assume you have experience with new parts not working.
The "modified" rod gives me some concern. I would first try to get a picture of a stock rod for comparison, or may be post a picture of yours for comment.
Did you make a detailed comparison between the booster you removed and the one from the store? The reason I ask is that the previous owner could have used one of the power brake conversion kits that were "designed" for manual brake pedals. If you swapped in a stock style unit then the rod could be pushed further into the booster unit causing havoc. Another thing to check is the mounting point for the brake pedal. The power mounting point is higher than the manual mounting point. I'm just throwing out ideas since it appears you have covered the standard bases.
You might check over at the MustangSteve forum. Scott is having very similar problems to yours.
