gunk in gas

Hi, I have a new to me Steplift with a 1987 150 hp BlackMax. When I removed the old fuel water separator to put in a new one the gas that came out was brownish, looked like phase separation had occured, and there were brownish specks/globs in the gas. I plan to replace the F/W separator and the inline filters. Should I get the gas tank (aluminum) sucked out (just dregs in there now, previous owner ran basically dry) or just be prepared to keep changing filters as the globs get trapped in the new filters? Any advice appreciated. Thank you, larry