This is truly an awesome looking project. Great work Cpt. Kipard. I only recently discovered the Skylon while reading about SSTO on wikipedia and decided to try recreate it in KSP. I have no modding skills what-so-ever, so I used mod parts from various packs. Mainly B9, KW Rocketry, RetroFuture and Hangar. It's been a lot of trial and mostly error. My version isn't quite as close to scale as yours, though. Made my fuselage using 3.75m parts (couldn't find a 5m cargo bay to my liking), but probably longer. It's length is roughly equal to 8 of the B9 HL 8m Cargo bays. The reason for this post is, that I recognize some of the flight problems you describe, with take-off speeds and mystery forces inducing yaw and roll, during ascent and re-entry. I still have these problems, but I managed to fly anyway. And I wanted to share these pictures as a fellow Skylon enthusiast. http://imgur.com/a/qwhvi
Thanks, I've seen them, but they were not of the scale I wanted. Yeah, sorry, my bad. I didn't actually mean to imply that they were caused by the same things. Just thought it curious that I'd had seen the same symptoms, even if it was caused by something different. And you're probably right about the size causing the yaw and pitch problems. I've had to use a lot of struts to keep it from buckling and breaking in flight. Probably didn't do a good enough job. That's all from me. Sorry, for the derail.