RE: I don't know this one..
It is possible to trim a plane for straight and level flight that is grossly out of alignment. But that’s all you will get is a plane that fly’s good straight and level. You say the thrust line "seemed" ok. To have a good flying plane these things need to be measured with a good incidence meter. Without checking EVERYTHING to make sure it's right to the designers specs, you will just end up going in circles making changes. For instance, at this point moving the CG forward MAY solve one problem but can cause two more.
With all the baselines in check and set right on the money, thats when you can start to make adjustments based on what the plane does when it’s flown through various configurations.