Toby, it sounds like you mostly have inflammation. Taking an anti-inflammatory like an NSAID or, better yet, quercetin and bromelain can keeps things cooled down.
I'd also just say, take it easy on the knees, brother. Aikido is a notorious milieu for people screwing up their knees. I would highly suggest you sloooow down in your movements. Get some proper principles and skills under your belt, especially with regards to movement of the knees. Such as...
1. The knee should always move in the direction of, and directly over, the foot.
2. The knee should
never extend past the foot.
You DO NOT need to strengthen your knees. Just like you don't need to strengthen your elbows. They are hinges, and nothing more. What you need to do is STOP
weakening the hinges. Stop putting undue stress on them.
I'd also say, do your class training in class, but for now, stop trying to replicate it at home. Far better to get some real fundamentals in your body, such as those gained by horse stances. Here's some good info on horse stances...
http://www.trigram.blogspot.com/2007...al-arts-2.html
And, again, slow it down. Better to make a few fundamental movements correctly that a thousand incorrectly.
Cheers...