tips advice questions whatever:

I'll start, I'm so into CAP its scary, all i can think about, got a late start but im catching up fast. Love IT, new platforms are amazing, sinking stuff (besides the limit) is incredible. I have a degree in drafting 1993 i think, and this shit is so far advanced from what our 2d wireframe cadd was

My Question:
I'm trying to make a snake run type thing, I understand the physics of it all, I understand when something crosses over another its merging 2 things. My problem is on this perticular snake run I am using the big transition low height quarters. I decided to use the entire tranny so I could do other things with my merging layer limits. So I have street pads as my flat, and they are under the lip of the tranny. half of it works perfect, around the corner it looks and snaps perfect into place, but at some angles/speeds it acts like it is not lined up (odd popups/bails) It is not my first go with the tranny's but usually I raise the flat up there for merging. I wanted to try some new things and not merge as much as possible.
Any Ideas?