Have you ever set up your tools and everything before you started running and did a tool change on the fly and just hit go and let it go? It sounds like you change your tools and re-zero them or something similar during the program or write multiple programs like I did before I got ahold of fixed tooling.
If your looking for really nice fixed tooling, check out the tormach tooling system
http://www.tormach.com
It is what I run and I love it, it only needs about 2" of clearance or a little more to make it easier.(or whats needed for the next tool if longer)
Maybe Im just following this incorrectly, Im just describing a rather simple way of setting all this up similar to how you describe.
I know your using the quill and R8 end mill holders, that must be quite difficult to change tools with the little travel there is there.
Jon