Hi Kim,
This may well be FQ toxicity and you've done well to find out about it and stop your exercise. Many people don't realise what has happened and try to exercise through the pain which can make everything a whole lot worse.
Try not to be 'wildly frustrated'. Your body has taken a hammering from a very potent drug - yes, it's effective and will cure just about any bacterial infection by preventing the bacteria from replicating. The downside is that its bactericidal action is also damaging your mitochondrial DNA plus it creates a lot of oxidative stress in every cell in your body. The end result is damage in your muscles, joints, collagen, organs, guts, skin, brain - you name it!
The important question is how much damage? A lot of that depends on your age, fitness and what insults your body has suffered before. By insults I mean damage from other pharmaceuticals or chemicals of some sort, pollution, bad food and alcohol choices, and also some genetic deficiencies. It's quite complex!
If you're relatively young and fit and this was your first course of Cipro you may well find that what the doctor says it true and the pains will decrease in a couple of weeks. Or a couple of months, or a couple of years.
It's a lottery which depends on many factors and the truth is that nobody knows the answers to 'how long' or 'how bad'.
If you go to this discussion on the site: http://patient.info/forums/discuss/fluoroquinolone-toxicity-syndrome-427305 (Pinned post by the Moderator), you will find some helpful addresses for sites where you can get information, help and advice. I don't know if you're on holiday now or were on holiday here in the UK but I'm shocked that you were given Cipro for a kidney infection. Was it a UTI that got out of control and had you been given any ABs before? Usually they prescribe Cipro only when Trimethoprim or Cephalexin (for example) don't work.
I suggest you find out as much about it as you can, starting with the link I gave you. If you're UK you can send in a report via the Yellow Card system (more people need to report so that doctors will know it's a serious problem). Don't be tempted to take Ibuprofen or any other NSAID as these can make your pains a whole lot worse. Your gut will have been wiped of the good as well as bad bacteria so start to look after it with probiotics (live yoghurt etc.) and stay off sugar and junk foods. Try to eat as cleanly and healthily as possible. The same with alcohol, your liver doesn't need any other toxins to deal with at the moment.
I hope this all makes sense and helps. I also sincerely hope your pains subside soon. be warned, though, that the cell damage can continue long after you stopped taking the Cipro so even the pill packets warn that you may get other symptoms or even tendon rupture months after you've forgotten all about it. Take it easy and be careful for at least a year. Watch you body for new, unexplained pains, especially in your legs, Achilles and joints. Hopefully nothing will happen - but oyu need to know that it might.
Good luck, feel free to ask any questions about it but there's loads of info on here in the various fluoroquinolone discussions (you'll see my name a few times!).