Thanks for the replies. He was better last night and actually made it to the pee pad each time!
The only time he was whimpering was yesterday morning while I was getting ready, but it was what I would consider constant. I decided to post the question because I wasn't sure if it was going to get worse and I wanted to be prepared this morning. He was whimpering this morning as I was getting ready again, but only a couple of times. I don't think it has anything to do with the vaccinations, I have rubbed and touched where he received his shots and there doesn't seem to be any pain and it doesn't bother him. I'm sorry if I didn't post the question correctly.
He got three shots on Saturday.