I have one of the older models (2004/5 I think) and on mine the flyscreen is definately zipped to the door so you can open with one zip.....but I can't off hand remember if mine has a mudflap on this section ( a while since I've used it) but I don't think it does, it must be on the newer models.
With regard to the rear guys I think mine has the same as yours and I think they are fine as the back slopes so maybe does not need the support the 'flat' front does.
When you say the rear guys are not symetrical do you just mean an odd number? From memory there are 3 at the top and then 2? lower down so yes you cannot line up the top guys with the lower but just need to make sure they are evenly spaced. I do recall that when pitching it was always the rear guys that I pegged, and repegged to get it right....have you tried shortening the guys that you say 'lift' the back of the tent...I think I always needed to have them as short as possible to get it to sit right.
Just had a thought, if the flyscreen is as you say then I presume the only option if you intend to use that as an in/out door is to roll up the flyscreen out of the way during the day. In fact I never used that as a door as such...it was either shut or guyed open with poles with the flyscreen up or down if the weather was warm.
Sorry I'm not much help but if I find out anymore I'll let you know.