I just helped a friend with his trimming of a glider that had it's electric motor in a nacelle that projected forward from the vertical fin. He had chosen to solidly attach it with downthrust because "most models need downthrust" and they usually had about 4 degrees but the designer hadn't drawn any on the plans. Bad news was it sucked and was almost impossible to fly. Good news is that the unbalanced prop trashed the motor mount and he had the opportunity to readdress the mounting setup.

The best advice for an experimental (and all prototype designs are basically a combination of many smaller experiments) design would be to make sure of one thing. Build your model so that it is as easy to adjust your thrust line as it is possible to do so. And approach your power applications on the first flights gradually or at least with extreme concentration.

There is a reason every major airframe mfg has at least one wind tunnel. And history is filled with many designs that needed modification after it's initial flight tests.