First question, feeling unclean, and wanting to protect yourself.
You are absolutely right in wanting to protect yourself. Remember a big thing for R for many of us a BS's is that we finally have to learn how to put our needs and wants first. This falls in that category I think. You don't feel clean, and need to feel safe. Who knows if strap on a condom and you feel safe the issue with the second question may go away voila.
I do want to say that if you have had sex with her very much since Dday without protection, that you have probably exposed yourself multiple times to whatever if anything she may have had, and using a condom at this point may be too little too late, if she truly does have something.
NOW - Finishing. There were times after dday that we both had trouble reaching the big O. H had issues with it, when he was still in contact (breaking nc) with OW, kinda one of the gut reasons I knew he was breaking NC. He would be able to finish though if I was facing away from him, and I know that he was probably transporting himself to thinking of not being with me, but hey it got the job done.
There were times where I as the BS had trouble with reaching the O, and with stopping the mind movies, and I gotta tell you I made it all about the physical aspects of sex. I made him make me the center of all the attention. For a while sex became more about fucking than intimacy, and making love. As I healed and got stronger, then I was able to transition back to more of an equal partner, and more about the whole thing, and the intimacy that came back was 10 fold.
I want to tell you a few things though Rolf. One it's perfectly normal to be going through all the feelings and emotions, and trials that you are as you heal yourself from this. It is truly one of the most difficult things to go through in your life. Do NOT pressure yourself to "get over it" and to "move on" and to "get back to normal" because your old normal is gone, and honestly if you do it right, and your wife does it right the new normal you find will beautiful, strong and loving. You will be amazed by it.
Secondly your wife is the betrayer here, and if she isn't doing anything and everything she can to help you, and not judge, and not pushing then she doesn't get it. She has to be absolutely on board with your needs and concerns, and if she isn't then you need to let her know that you don't accept her only being partially in on R. Sometime the WS needs a bit a hand holding and guidance to and the BS being very specific on what they need. Don't be afraid to ask for it.
Lastly HB, and sex can be a HUGE part of healing and recovery for both of you, but may come and go, as you heal and get stronger. Allow it to work it's magic. We are 5+ years out and I can say that our sex lives now are even better than they were prior to Dday, the A, and even after.
(((and strength))))