bigtyme,
Either you have the wrong motor mounts or the wrong frame mounts. I have the small block (327) mounts on my frame and with the S&P conversion plates and stock motor mounts they fit a lot more snug than that. I would cross reference those parts again to make absolutely sure you have what you think you have. Unless all this is different for the '69, which I don't see why it would be.
As for your header problem, what brand headers are those and what part number? You have to get the specific headers from Stainless Works to clear the stock steering box with the S&P plates.
The part number is..."CALS1SB" for the regular finish and "CALS1SBP" for the hand polished. These are specifically designed to work around the stock steering box USING the S&P plates. Some pics for reference. Header #1 looks like it's close to the power steering box but it's really not. It's just the angle that the picture was taken. There is actually 1/4" of clearance. God speed my friend.