They don't look clogged, the main thing is you can't really tell if they will seal until you re-surface the sealing surfaces and measure them for flatness with a straight edge and feeler gauges (less than .003" variation). For the busted bolt stub, try heating the area around it and see if that helps get it out. Don't heat the bolt, just where it's screwed into on the mani. You want that area to expand slightly. These jobs are always tricky, not sure if the vise grips is the best plan, maybe cut a slot in it and use an impact screwdriver instead. I have never found vise grips to help with removing the remains of stuck bolts. Heat + patience.
Then, get thread chasers and really clean all those threads out. Not a tap, but thread chasers. I used them when I had to replace the cyl heads on my old 4.3. It took a fair amount of time to make sure all the bolts would thread in right. Thread chaser, bit'o carb cleaner and compressed air...wear goggles of course.