Those aren't bolts at the ends of the manifold, they're alignment studs that screw into the head. Some people remove the studs and substitute bolts, but it's not necessary and might contribute to warping the exhaust manifold if they're overtightened.
The only engine that must run a filter or a bypass line is the late-production 261 that has been set up for full-flow filtration. You can simply remove the flex lines and plug the holes in the block on all the bypass filter systems. That subject has been beaten to death by several people here, so you should be able to find a ton of information on full flow filters with a search. At least some of the info is actually correct.
Jerry
