just had my carb rebuilt and found sand-sized flakes of rust in bottom of bowls. so i came home and pumped out some fuel from the line into a clear jar, and found more of the same. any suggestions as to where this could be coming from? boat has an aluminum tank and merc. fuel filter so not sure where this could be originating?

Probably your fuel supplier, ie gas station. The crappy fuel that is now on the market is good for a couple of things. Collecting water and cleaning and rotting out fuel storage tanks....

shouldn't my merc fuel/water seperator filter that stuff out?

It should. How old is your filter. With the methonol content in the fuel out these day's it only take a short time (couple months) to act on the filter canister itself depending how long it has been in there. Most likely it is out of the tank you filled the boat at. It will make its way thru the filter. There is also a bacteria called HUM BUG that is being found in this modern day fuel. From what I have read it forms in a couple months of fuel storage. It takes a very high micron filter to pull it out. I had this problem myself with some diesel fuel in my p/u. Pulled the filter it was a nasty brown rusty looking crud that clog the filter in less than a couple weeks. You can research this on the web. Have not found a solution yet except some super high micron filtration system. I have been using marine fuel treatment in my boat on every fill up and have not seen it show up there yet. My p/u is another issue. Changing filters everytime I see the fuel pressure start to drop. Good luck

Install a good in line fuel filter besides what you have and change it often . Buy your fuel at a different place.