Sure caot the threads if you like, but I woud do it to the holes and not on the bolts themselves. There is a risk that the neverseize will contaiminate the gasket area around the bolt holes if you treat the bolts instead of the hole.
I would clean out the bolt holes, surface-oil the bolt hole threads, and wipe down the head and block surfaces with paint thinner. Use no sealants on the head gasket; goes on dry. I take two of my old bolts and cut the heads off of them to use these for re-assembly guides (screw them in the holes, slide head down on them.)
As far as timing goes...all should be well. Once you re-install the tensioner cam pulleys, and chain guides, rotate the crank slightly backwards and then return to tdc. Do the cam notches look aligned? Yep? All correct then.
Cheers, Blake