You should do both sides. Muratic acid overnight works wonders if your finances are tight and there is enough good wall thickness left.

Yup, I am "Boating on a Budget"! After the acid soak, do I use baking soda, or something like that to nuetralize it?

Let them soak, then run a stiff wire through the passages then let them soak some more. Finish with a thorough flushing with clean water.

The acid wash will without any doubt clean all the rust out of the manifolds, but I have gotten into troubel leaving them in the acid wash too long. What happens the acid will also eat good metal along with the bad. Often you may have to maching the gasket surfaces again to get a good seal. You will be surprise how clean you can get them with hard wires, screw drivers air then flat fise the gasket surfaces and your back in busness. As soon as you take them apart you will see the water passages restricted. And when your all done you should try to water test them . Run hot water thru them, and look inside of the exhaust ports they should be nice and dry!
Good luck and post what you finally end up doing.

Well, got a new manifold, the old one had a 01-89 casting number, pretty rough. However, I am having problems getting the new manifold on. It almost sems like it is warped, if I get the middle snugged, the outside bolts bind. Any ideas?? It's brand new. This is turning into a nightmare, should be pretty simple.

Did you only buy one manifold?
We are talking exhaust manifold correct ?
Typically you would replace both reason being if one is gone and the other is the same age it is probably in the same condition.
Lay the manifold down on a flat surface, or somehow inspect it with a straight edge. Then lay the gasket over the bolt holes. The bolt holes in the manifold should line up with the gasket. On the exhaust manifold , you may have the gasket upside down ??????

Another item I forgot to mention. The manifold is quite heavy and awkward. Occasionally I will put a stud in the motor with a slot in it for removal. Put the gasket in position, put some grease on the other end of the gasket so it lines up. The slide the manifold on and catch a bold on the other end. Get all bolts started, then proceed to tight the manifold up. Start in the middle and just snug eveything up.

Gasket lines up, I can get all the bolts started, its just when I draw it up, the end bolt on the front binds, like the hole is a little off. I shouldn't have to open it up, I wouldn't think.

Well, I got everything on, the bolts were a little long, the new manifold was a little different, so the bolts were bottoming out. But that did not fix the problem, the coolant HOSE was FULL OF GUNK!! I can't believe it, I meant to check the HOSE earlier! What a MORON! Anyway, thanks for all your help, and sometimes you don't get the WORST, even if you expect it!