Rusty water jackets. what to do?

[VeeDub]

My vr6 engine sat for years and rust has formed in the engine blocks water passages. Ive flushed it twice with Prestone cooling system flush, following there instructions of course. After a short amount of time the coolant turns brown, from the rust still left inside the block. Ive done a google search. and have turned up a few results, heres one - http://www.evapo-rust.com/. Prestone also makes another flush for "neglected cooling systems".
I was wondering what you guys would recommend to fix it?
The water pump went this week so the motor has to come out to replace the pump. I'm concerned, if I don't fix the problem the new pump will fail prematurely. Money is tight so I prefer to not tear down the engine. Ideally another flush product would be better- as I could use the leaking, but still functioning ( ) water pump to circulate the flush before the engine removal.
Any thoughts?

[Maverick]

My Maverick sat for 19 years before I got it. The block cooling passages were really nasty. I rigged up a garden hose to the coolant intake and left the oulet open. Started the engine and let the hose run just fast enough to keep the engine from gettin too hot. Let it run that way till the discharge ran clear. Wasn't a problem after that.

I can't recall for sure but I don't think I had the water pump belt installed.

A gargen hose connector will screw onto a 3/4" pipe thread.

[VeeDub]

I stopped by a Mercedes dealer today and ordered this http://www.bimmerspecialist.com/usa/par ... 025%2011/3
Found out about this stuff on a Ford site. This guy used it to clean out his 289 engine and was impressed with how well it worked. So I researched a bunch on this MB part #000 989 10 25. I'm going to give it a try.
Its a citric acid flush. Some internet sites were saying "any citric acid powder will work" (grocery store baking isle??), but I'm going to spend the $22 on the Mercedes stuff. I'm not that cheap

[Basement Paul]

Let me know if it works out. The Caddy has had the same affliction since I put that old motor together. I flushed a few times and there's still some brown residue that always shows up.

-BP