I have used the potion-swap cheese to give my solo Cleric/Theif a familiar.

Even though my Rep is 15, I now have guards chasing me all over town. Is there any way to avoid this?

Go back to a saved game prior to using the cheat.

what guards?
Cowled Wizards or Athkatla Guard?
do they come when you cast spells?

No, it's not casting related. It's due to the cheat. I wonder though, if I can get past the 1st round of guards if that will be it, or will it go on and on?

i've never heard of guards chasing you around because you have an illegal familiar

i always use this trick to get one, but never experienced any trouble

Go ahead, break the rules, but don't get caught. I think that's just the right punishment for your behavior. :D

I doubt very much it's related to the Familiar, i've always used the potion-swap trick to get myself a Familiar when playing a non-mage character and never experienced any problem. If it's not the Cowled Wizards it's a definate bug. Have you the official patch installed?

if I can get past the 1st round of guards if that will be it, or will it go on and on? An army of guards will spawn in anytime you switch districts in the city.

Well, I'm on a Macintosh with OSX, so it may be a newer version. It must be the potion Swap, because, as I said, I had a rep 15 at the time...

What made it worse it I (like a genius) rely on quicksaves and autosaves, normally. I had to redo a week's work.