Several issues are involved here.
My first question is how did you determine you have rust on cylinder wall(s) and on intake gaskets?
My second question is how was engine stored (in a garage, outside, under hood, etc.)? What was the state of engine assembly (or disassembly) during this time (and for how long)?
First of all, any uncoated steel or iron will rust fairly quickly. In most cases, as long as rust hasn’t pitted or etched into cylinder wall or valve stem, you should be good.
Having straight water (rain, cleaning water, etc.) in cylinder causes a lot of (and deeper) rust.
Second, need to find the source of water moisture.
Driving car with a “known problem” will make things worse in more ways than one. If there is a problem, now is time to fix it.
Water entering through the carburetor holes is (I think) the number one source of water entry. At any one time, there is at least one intake valve open. Cylinders with rust in them – will also need to check the valves of same cylinders for rust as well – and that may require a valve spring tool to remove valve springs to extract valves. Note: try to avoid removing more than 1 valve spring at any one time.
Usually if water got into engine via carburetor holes then generally water has been sitting on top of other valves, as well.
Intakes do not warp often. There is coolant passageways on front and rear of intake (the back ports are blocked off). If intake (or intake gasket) was to leak coolant, it generally will leak coolant into oil pan, and not the intake ports.
Cracked/warped cylinder heads and/or blown head gaskets will allow coolant to get into combustion chambers when engine is running and just after engine is turned off. The middle four cylinders are ones most likely effected by cracks/warpage/head gaskets.
You mentioned “After freeing up the engine twice” did you mean coolant froze or engine would not over when checked?
