My first step would be to see if things aren't too tight when your foot starts to hurt - as 10 wheels said, feet swell. I solved excruciation pain by simply loosening the laces and that was with modern clipless shoes.

Then I'd try a new innersole just to see if it is just your old shoes wearing out.

Seeing you've been riding this way for so long, it's probably just something wearing out (not your feet is it?).

I converted to toe clips a couple of years back after pfaffing about with clipless and SPDs for a couple of years. I much prefer them for the riding I do and no, I don't get foot pain. It's hard to get decent shoes that haven't been built to take under sole clips - I wear BMX shoes, but skate shoes also work. The massively hard sole you find on modern shoes is mainly there to support the undersole clip, as evidenced by the shoes I wear - the clip version has the hard sole, my version has simply a stiffer sole than a normal shoe.

Richard