If my new furnace woke me and my wife up at two am, It would be out of there!
I have not looked yet but Rheem probably has a web site with a question and answer section. Give it a try!
This is not right. As it was stated before, document everything. If the dealer you bought it from claims this is normal, insist on having a Rheem factory rep look at it. Do all the requesting in letter form. Tell the factory rep you want his findings in writing.
If you do not get satisfaction, let the dealer and Rheem know that you plan to take this to court. Tell them you plan on showing a Judge a tape of what your "NEW" furnace is doing and let him/her decide if this is normal! The fact that you have this on tape will get the attention of the dealer or Rheem or both.
Do all of this in a calm manor because if you go this route, they will probably agree to fix the problem before it gets out of hand. If not, you need to come across as the reasonable guy!
I would use a video camera with a date and time feature. You would need to measure back from the furnace say, five feet,(write down the measurment), set it up to run and let it go. You may have to try this a few times to catch the problem.
I hope that you will have to do none of this but, if you have to, it is better to have it down now than try to go back and recreate it.