Pulled Out Lower Intake - Coolant and pieces of rust on top of heads

They area you are referring to is the lifter valley, where the lifters, and pushrods are, and the cam is right in the center if you look through the holes.

Take some paper towels and ttry to get as much coolant and dirt as you can, if you have a Wet/Dry vac it will also work very well, clean the gasket surfaces on the heads and tape them off whilw working so nothing falls into them, if the intake will be off for a long time, I'd tape up the lifter valley also, or atleast put a clean rag there (just don't forget to remove it all before installing the intake).

If there is enough bolt sticking up from the head you could spray it with some penetrating spray (try not to spray it all inside the motor and head) or heat it up and try to twist it out using a pair of vise grips, just go slow. If that doesn't work or the bolt isn't exposed you could try using a eazy-out...make sure then lifter valley and any open part is covered so not metal goes into the motor while doing this.

I also suggest changing the oil when you are done to make sure you got the coolant out.

Good Luck!