I bought my 4701 couple yr ago. I have not had the collection of problems you have, but I have had the white smoke and rough-running bit. In each case, this was on cold days, in the range of below 15 deg F. I read somewhere that this can be caused by water vapor freezing in this or that part of the exhaust train. Not just in the 4701. However I have not verified this.
I have found that 1200 RPM at idle or operation is too low. Up nearer 2000 or so works well. I live on very steep terrain and must often run at 1500 RPM due to safety [tipping over danger, etc.]. Therefore, I can rely on a regen' around every 30 hours operation.
It does sound as if your problem is more than what causes mine. Good luck with the dealer, my service manager at the dealer had no clue, or said he didn't, about what was causing my white-smoke thing. In fact, he asked me to contact him and tell him what I found out, when I did, and what I did to "fix" it. I wrote Kubota, who in the past with other tractors have responded with good info', and the reply was that I should take it to the dealer's service dept. Useless.