I am not quite sure what you are saying, but if I understand correctly the reason that your iPod is running slow is because you have many jailbroken apps installed that run in the background. Examples of this are SBSettings, any Themes, etc..
I have jailbroken my iPod many times and also jailbreak other iPods and set them up with the best jailbroken apps. I would say that the only true fixes to your problem are A. Uninstall all jailbroken apps (slight chance of working) B. Restore. I would highly recommend a restore, and re-jailbreaking it should not be a problem due to jailbreakme.com