Your knees being sore is most likely due to the position of your knees now that you sit further back.
If your knees are further rear relative to the pedals axle when pedaling then you have a problem. Remember, its supposed to have a more upright riding position as well, so initially you will feel as if it is short this would be overcome by more time on the bike.
I would give a 100mm stem a go or go and get a proper fit done. It would suck if you have got the wrong size frame. This is currently a dilemma i am facing before i lay down my hard earned on one.