If you hadn't been to vet, I'd have suspected UTI. If not that, kidney or bladder stones? Definitely thyroid check.
Is he getting the same exercise? Can you do more so he's really tired at bedtime?
Any new medications? Change in food?
If it were something icky like a mouse, his buddy would be bothered too... but it could still be outside nocturnal creatures suddenly stopping by.
Hope you find the cause. Losing sleep is not good for anyone.