This is just my opinion and it might go against what other people think, but it works for our family.
Yikes - if he is getting over being sick and cutting a bunch of teeth, then I'm not surprised that he is having difficulty going to sleep. I know that when I'm sick or feeling badly, I really like to be a baby and let my husband take care of me. Knowing this, the one time my baby had a cold and when he had a fever after his 4-month shots, I decided that all 'formal training' was out the window. If he wanted to be held all day, he got it. If he needed to be rocked to sleep to go to bed, then so be it.
Fortunately, you should be able to tell the difference between him being sick/hurting and just simply not wanting to go to sleep. Personally I see no problem soothing him when he's feeling ill and hurt, but if it isn't that (and it were my kid) I'd let him cry it out (going in to check every 5 minutes with a pat on the head but not talking/picking up, etc.).
Good luck to you - I know these times can be really tough!