What are your recipes? Nothing I ever brew ever hurts at all, including test prop at 100mg/ml using 2/20 BA/BB, soybean oil, and a .22 whatman. I cannot see any reason at all for your homebrews to be giving you pain at only a 2% concentration of BA. That's an excellent concentration, in my opinion.
I would not recommend making any of the above without BA nor should it ever be necessary.
And no, you will not cook the BA out of solution.
Anyway there's a good reason that BA is in there.
Couple of questions:
What kind of filtration system are you using?
On a level of 1 to 10, one being only the mildest soreness, ten being crippling pain that prevents movement, sleep, and aspects of regular life, where are you? Typical UGL mulekick crap will probably have you at a 5, but dirty gear will put you somewhere between 8 and 10, often accompanied by flu-like symptoms. I typically find that when I have real problems it is usually a filtration issue, and never anything else. This can be solved by a second filtration.
What kind of oil are you using? Perhaps you are having a reaction to that?
I really do NOT think that your problem is the BA content, unless your body just happens to have a particular unfortunate negative reaction to BA.