Well, took a ride with my saddle raised up, and seems like it sorted things out! I raised it an inch, and rode for about 3 miles. Then went up another 1/4", and rode about 10 miles, and lo and behold, not only does my knee not hurt like before, it feels better now post-ride than it has for the last couple days I took off to rest it (due to stiffness I suppose).
Still, a pro bike fit is in the cards--will be switching over to clipless soon as I get the funds and will do it then.
Thanks for all the replies.