I've done it three times (I think, maybe 4), it's fine, what bad things have you heard about it? The loos were a bit grim last year but that's true for most races, the support is good for most of the course, the route doesn't really take in Edinburgh but is pretty enough. The organisation itself seems pretty good, the pens at the start work well, I've never had a problem with water/tshirts/medals/etc. The only area I recall hearing people complain about is the coaches back at the end, I have never got one so can't really comment on that.
It's a great race, have fun! I got the train back last year, I think I was stood up but it wasn't crowded like a commuter train over here, there was plenty of space to move. I'm sure I could have got a seat if I'd tried.
And you two have no problems when you run? I would normally go three or four times and have constant trouble when I run - is it just this simple? Am I just doomed by my usual regularity/lack of meat in my diet?