going through the same put, put, put sound right now.
this is what I have found out....basically the factory exhaust studs (at least on my motor home 440) are pipe thred and go into water jackets.
When I got the headers some of the factory studs where really warn and I replaced all of them with header bolts. risky move on my part.
One side held water the other side had 2 water leaks.
Long story short the header bolts where not as fat as the studs, on the passenger side I changed back to all studs I even had to get one stud custom made (larger) at the machine shop at work.
Before i put the studs in I cleaned the hole with acetone and put hi heat RTV on the stud careful not to put RTV on the tip that goes into the head.
I am running headers and I used 2 fel pro gaskets, before I put the gaskets on I used RTV on the head and the gaskets and the headers.
no lots but a nice coat.
The passenger side is just fine....
My driver side all header bolts, held water but developed a exhaust leak with the 2 middle ports.
I am now using 2 studs (in the middle) and the remaining has header bolts all with RTV and 2 fel pro gaskets.
Its all holding water but I have not fired the motor yet, this week.
So, I guess i'd suggest with stock manifolds use studs and a gasket with RTV.
good luck!