You need to look at a couple of things. One, like obnoxious stated, get a quality plate.
Second, the run out you are seeing does not sound unreasonable, however, are you certain it is seating properly? Do you have a PTO designed specifically for a flex plate?
Also I will add,it is important to check the crankshaft thrust run out. The harmonics will not come from a flex plate gyration, but it can weaken the flex plate center causing a very unfortunate failure.
GT