I've had almost 2 weeks off after finishing W3R3 with bad knee pain. With rest, ice and anti inflammatory drugs they're almost back to normal again.
Would anyone who has had a similar problem give me advice on whether or not to carry on where i left off or go back to w1, 2 or 3.
I don't think the issue should be whether to carry on from week 4 or go back to 1, 2 or 3. The issue is whether your injury has healed sufficiently to start running again. You say that they're "almost" back to normal again. It might be worth giving it a little more time until they are "completely" back to normal.
Sorry for being a downer, but I'm slowly learning the hard way that it's well worth the time to listen to your body 
I echo Tomas' comment. Make sure you're ready, then why don 't you try where you were before, you might be surprised . If you struggle , stop & go back to an earlier point. This is your race, no-one else's, so it doesn't matter. Good luck with getting out there again x
I would agree with Tomas and MarlyParly- don't run if your knees are not yet 100%. I have struggled with my knees since I started this programme in January (although I do have an existing injury).
It was literally 1 step forward and 2 steps backwards for me as I tried to carry on. I am two runs away from Graduation but my GP has just told me I am not to run for at least 2 months to allow the knees to fully heal.
When I began running, I 'ignored' the advice to go for gait analysis and get the right shoes as I couldn't afford expensive shoes. However, the money I have spent on various knee supports, KT tape, physio treatments ect ect over the months would have easily paid for the expensive shoes!! This may not have completely solved the problem but I am now convinced it would have made a huge difference.
I am determined to finish this programme but will rest up for now.
Don't rush back into running and risk further and worse injuries.
Once your knee is better if suggest going back one run then keep on going. My hubby had a similar problem at the same time, after resting it he bounced back
I had the same issue and took 2 weeks off. I started back at Week 1 and just finished week 3 day 2 with no knee pain. Good luck!
Knee problems!!
Sharp stinky pain in knee
The Jelly Battle of Wounded Knee
Bad knee....repeated run, all good! 
Knee-naw, Knee-naw
