I passed up the chance twice to get X6-88 as a companion cause i was trying to get full affinity with Codsworth and now i can't find X6-88. I've searched all over the institute...anyone know where he prowls around at?

Try looking in the SRB section.
He hangs out there, once he is available.

If he is not there go look over by nordhagen beach towards libertalia. I found him there wandering around.