"I'm a bit concerned about long-term damage to knees by sitting in seiza, although right now my knees don't hurt at all."
I'm glad you're knees don't hurt right now. However, I reiterate, if you're concerned about long-term effects of sitting seiza, go see a doctor.
I'm afraid that sensei Ledyard got the impression that I was implying that there must be something drastically wrong with you if you can't sit in seiza w/o pain. That's not the case. What prompted my suggestion was your description of having pain for one or two days after practice. That seems
a bit more serious than the normal problems that most people have with seiza.
If you have good health insurance, seeing a doctor can't hurt, and it may help prolong your practice for many years to come. You may want to see a sports medicine doctor instead of a regular one. Sports medicine doctors will help you enjoy Aikido, while a regular doctor may tell you not to do it.