When you say filters, are they the replaceable inline type filters? Like a "whole house" style or something? I would bet thats where the chunks of stuff came from, its probably calcium buildup or something that hardened up while sat over the winter.
As for winterizing, I'm paranoid. Not so much that I'll pay the dealer $150 to do it (though I have in a pinch to save time), but enough that I blow the lines out with the air-compressor AND I run antifreeze through the system. Air is free, antifreeze is cheap, process is easy, just have to have the time to do it is all.