I'm rebuilding an inline 6 and the water jacket has a lot of rust. I've removed as much as I can with brushes, so the next step is to fill it with vinegar or Evaporust to clean out the rest. The problem is that it will probably be months before I can get it running on a test stand with proper coolant. So, what can I do to keep the rust from forming again on all the fresh, bare metal inside? Or is the amount that forms not going to be a concern? Yes, it would have been ideal to have the machine shop dip it, but they only sent it through the washer and only told me they weren't going to dip it until after they had machined everything. So it is what it is.
I did a flush with Rust 9-11 (like Evaporust, only a concentrate and therefore quite a bit cheaper). Two one day soaks interspersed with plain water flushes in between. It turned out well in my opinion. I was able to run my engine right away, but I don't see a problem leaving your engine sealed up with the solution still in it. Just flush it again with clear water befor use. (Don't try that with vinegar, because it's an acid and will keep eating away at the base metal.)
Remember that once the engine is together and running, you could introduce some chemicals to your cooling system for a final cleaning.
Clean it with vinegar or citric acid, flush with baking soda to neutralize, then run a water pump lubricant mixture through it. The pump lube should help prevent rust.
I would squirt some Gibbs lubricant in there. It will prevent rust, but won't foul up the coolant later.
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