Thanks for the suggestions. The Boy has checked and adjusted all the obvious things on this bike. He's got 10+ yrs in the bike business and fitting bikes, and has meticulous fit on his own road bikes, so we are confident that the fit is ok.

We measured the Q factor on the Ult 9sp bike and the Ruby seems to actually have a wider Q factor, by a few mm.

We did notice that the 105 fd seems to be stamped deeper on the outboard side than an Ultegra fd. We are going to try an Ult fd next. It may not need to be positioned quite as far out to clear the chain.

I'm using older Ultegra spd pedals. He put 2mm spacers (washers) between the pedals and the cranks to see if that would make a difference. I do have a tendancy to turn my right heel in a bit while pedaling, but we adjusted my cleats and I don't hit the crank with my ankle. I'll check the cleat position again and make sure they are not too far to the left side of that foot.