Sorry but I don't quite understand your question...From what I can understand you experienced side effects from the kratom, and now you are wondering if it will start working better after abstaining and then going back on it?
I don't see why it would have less side effects the next time you start back up, if it doesn't work for you don't use it...but IME the more you expose your body to any substance the more likely you will adapt to the side-effects...which is a double edged sword.
When I first started taking oxycodone I only got side effects and never imagined I would ever want to abuse this substance...same with tobacco and cannabis, they all just made me feel like shit basically the first few times I tried them...and it took a lot of peer pressure but eventually I ended up loving the drugs that I thought I could never love.
But maybe thats beside the point...although in your case I am not sure what to say, you have to give more details about your previous use, other medications, and reasons for taking Kratom...please enlighten us.