Hey in my experience my HS coach DIDN'T CARE if we had shin splints so I used to just run on them! But I don't suggest it if they're really bad b/c they can get to the point where you have to wear this cast thing from the doctor... I never did though but I had teammates that did...
What I suggest in the meantime and my college coach has us do this...
Get on a stationary bike and do your run via there... so push it hard on the bike...
doing sprint intervals on the bike really does give you a great cardio exercise and keeps you in shape while you're waiting for you shins to heal...
ALSO DO water running... it's really hardcore if you do it for like 30-45 minutes and you keep perfect running form in the water...And waaaayyy less impact...my coach always says never just sit around if you can help it...oh yea we did the water runs with floaty belts so the impact was even less but you don't have to :-0
As far as how long to wait I don't know... just keep icing them twice a day if you can spare that... and just ease your way back into actual outdoor running...run in grass and not pavement to reduce impact... STAY AWAY FROM THE TREAD MILL IF YOU ARE PRONE TO SHIN SPLINTS it is the worst!!!!
I think I just got used to my shins hurting and then they eventually either go away or the season ends :-P But baby them as much as you can... I believe you can build up a tolerance... I had no other choice.
I too experienced the knee problem thing b/c I ran for 365 days nonstop in competition mode...badd idea... darn coaches. I had to do knee therapy for a while so if anyone wants any of those nifty exercises let me know... they're mostly strengthen exercises...
Hope it helps a lil bit.
Jaz
PS so I guess the answer is they usually went away for me when I stopped running so I guess the answer is no they don't really ever go away you kind of get used to it and ignore it

And do the exercises they help!
There are two kinds of people that amaze me -- those that know absolutely everything and those that know absolutely nothing.