It is very difficult to give you a reliable answer from a distance. In general, if you built the PT-40 from plans and followed them to the letter, alignment should not be a problem. Did you make any mods in the way the wing is fastened on such as changing to bolt on versus rubber bands or make any changes in the way the wing sets on the fuselage? It could be that the wing has to high an angle of attack; if so put a shim under the trailing edge to raise it up. You could have the thrust line seriously off (i.e. built in some upthrust instead of down thrust). I'm sure that there should be someone in your club who could be trusted to get you off to a good start, check out some of the older members who have been flying a few years. In general, a PT40 is a very stable and good design that almost flys itself with the correct CG location.