headers ,etc., questions

Question #1 .... Yes
I like the entire TTI set up myself.
Question #2 .... Have not tried them.
Question #3 .... If the header you install are OK'd by the maker stating they will clear and automatic and a manual trans then it should be just fine. The exhaust piping should not be an issue. It is far enough away from the linkages not to be of any concern.
Question #4 ... Not sure but I do not think it is possible to port the smaller exhaust manifolds to the larger size. You need a gasket to check this.

4b .... I have read several times that the extra expense and actual power return on extreme honing wasn't worth it to do. UNLESS you are racing & looking for every last .001 second.
Pricey will low yields.