Re: Knee pads?
I never wore knee pads for Aikido or Aikijujitsu training. I did wear them, for a time, when I wrestled, and my experiences were similar to Mary's, in that, if the knee pad was secured well enough to stay in place while I was moving and training, it did bind. For me, I ended up with some heat rash from time to time as well. I did use some hard shelled "tactical" knee pads in SWAT, and they worked very well, but they would be too bulky for your use.
I am pretty big on training without a lot of extra padding or gear and toughening up your body, as having a conditioned body is often of huge benefit when bad things happen and a real attack, rather than a dojo training session, occurs. However, there is a huge difference between some muscle and tendon soreness from working and stretching in positions to which you are not yet accustomed or at greater intensity than that to which you are accustomed (the "burn" or "post athletic" soreness) and the sharp pain of injury. You indicate that you have injuries. If you have problems with your knees, then take care of them and yourself and do what you have to in order to protect yourself. You want to spend time in training, not in post-operative recovery after a knee repair. I have a very high pain tolerance, and, in the "heat of the moment" in training, sometimes I ignored a little more pain than was normal during an intense workout and paid for it later with painful (and probably preventable) injuries. Sometimes "cowboying up" and "pain is weakness leaving the body" helps you through rough physical training or real world conditions, and sometimes it is just a mantra of macho BS. You have to decide for yourself which is which and what applies to you.
Good luck in your training. I will tell you that, when I have students with injuries (as I frequently do), I appreciate them telling me about them. We try to minimize impact to the injured area of the student. Also, there may be some specific techniques that you will have to modify because of an injury. For example, prior to a knee surgery I had several years ago, there were some specific low level silat techniques that I could not perform without having a torn meniscus cartliage basically lock up my knee. Wearing a brace and modifying my motions allowed me to continue training. Your instructor may need to work with you in regard to the range of motions to which you should be subjected at this time, and maybe work up slowly to being able to doing everything "correctly".