1998 Acura Integra Engine vibration

I just rebuilt the engine in my integra using the Helms manual. When I pulled the pistons I did not keep track of them and got them mixed up. So I installed them back in, in any cylinder. The engine was honed and the pistons are the same oem, I used after market main bearings, rod bearings and rings. I so far have 800 miles on it, mostly highway miles (found out that constant speeds are not good for break in, too late) anyways I have a high frequency vibration, that I am picking up from the engine. Could this be from mixing the pistons up and maybe the engine is out of balance or should I look elsewhere? I did a compression check even though the engine has only 800 miles since rebuild and have 125 psi in all cylinders.