was diagnosed with lupus about 7 years ago, it's affected me in various ways, including joint invovlement, cutaneous vasculitis, raynauds syndrome, and pleurisy. plus i have the associated hughes syndrome, which basically means i've got sticky blood and a few years ago had a mini-stroke. i also take hydroxychloroquine but also anti-coagulants regularly, and steroids as and when, though at the moment i'm pretty much in remission.
however, there's no reason at all why you can't run, in fact, i did an ironman this summer. a few things to bear in mind though:
1) suncream - really really important. when i was diagnosed, it was a couple of weeks after doing an 80M run over 4 days,in the sun and they think the sun might have been what triggered it. you can get sunscreen on prescription if you have SLE (though if you have to pay for prescriptions anyway, you might be better off getting it OTC!)
2) make sure you drink plenty when you exercise to avoid dehydration. this can tip you into renal failure if you have any underlying problems.
3) because i've had problems with clotting i try and be sensible when cycling - ie don't go to places where no-one will be around in case you come off etc etc. prob less of an issue for running, but cram tags or a medic alert with your medication on might be useful.
4) if you take steroids, be aware that your immune system can be a bit compromised, and be sensible about training. e.g. last year i got a chesty cold, ignored it and went training anyway, and ended up in A&E that evening with a pneumonia and a collapsed lung. i am endeavouring to be more sensible this year!
5) if your joints are sore, try swimming because it's non-impact. even cycling is better.
6)don't feel sorry for yourself. it's completely counter-productive.
hope this is useful, if you have any more specific questions, you can drop me an e-mail through RW if you want.