I like what you are doing there John.
I have a Maggiolina ... which is great for sleeping in but has the same little problems. The flap at the bottom of the zips and the gap in the bottom of the zip which is against the mattress.
We have been out in it in some really bad weather and had little to no problems with wind or rain, but the entrance needs the improvements you are doing. Are you planning to leave the awning up in bad weather ? I am interested how you are attaching the awning to the roof. My Magg has a rubber seal all the way round the top on the inside and wont allow extra thickness when the roof is closed.
Me and the wife use a duvet ... tend to get hot and can throw it off as and when necessary, imagine a bag would be the same after a while ... but less bulky.
Rob