Boy do the "69 Windsor heads" bring back memories of the "bad old days"!
You know, back when the early Windsor heads were the best a Ford guy could hope for in an inline valve head! You know, the days BEFORE 25 choices of aftermarket heads, in BOTH aluminum and iron!
To answer your questions: The heads should have the holes for the later model accesory drive.
Yes they will make good HP if the port job was good, addressing the shortcomings of the stock ports. A lot of guys went real fast "back in the day" on modified stock stuff! I personally would not waste my time & money on modifying stock heads with the present availability of great aftermarket pieces but since you got these for free{!}

, GO FOR IT! The 2.02 valves and probable milled high compression would work good on a high revving engine like a 331 should be.
One potential problem, if my memory serves me correctly there may be some coolant passage differences and I think the early Windsor heads had an extra bolt or two at the corners of the intake. Plugging holes and creative gasket use can solve these issues though.
Make it happen! The price is right!
