I like to iron the covering and install the tail feathers and trial fit the wings before I do much else. That way if there are any major alignment issues, I can deal with them (either by sending back of fixing the issue, depending on how serious the problem is) before I look at the engine installation.
Also that way, I can consider the thrust line of the engine. I've had a few (of the cheaper) ARFs where the engine thrust line was way too high and I could modify the mounting points to suit. One particular example was on an ARF that I see regularly advertised in this forum. The engine mount is about 1" too high for an upright engine and the design is such that an inverted engine just doesn't work. This particular plane also has an issue with the carby being about 1" above the fuel tank. By lowering the mount, the plane flies a lot better and the motor runs a lot more reliably.

I find that a good stand alleviates the problems that you allude to with the tailfeathers getting in the way during engine installation. I use PVC pipes in an X configuration for this.