I've had issues with this myself. I discovered early on that Milo was super active at night, and quickly decided not to let him sleep in my room while I slept. This eventually turned into a nightly ritual of him meowing and pawing at my bedroom door for hours, hoping to get in. Lonely? Probably. Too much energy? Most likely.
The two changes I made were making sure I played with him for as long as I could before going to sleep (which would wear him out a bit, and allow him to get into a sleep-at-night habit.), and to put up a compressed air canister with a motion detector near my bedroom door. The compressed air really helped, and I use it on occasion to help reenforce the training. The playtime at night also really helps, but he still meows on occasion.
I know you may not be sleeping in your bedroom, but perhaps your kitty can go into his own room at night, separate from you? The air canister would help in that situation (I bought mine on Amazon, but I've also seen them at Petsmart).
Good luck! I definitely understand your frustration. Being sleep-deprived doesn't help anything...
MJ