I agree with Neil on the overheating issue. I'm not familiar with the Chromegatrol although I do get asked from time to time how to use one of our timers with that enlarger type. Switching the mains would work, but you may run into problems with reliability because the power supply wasn't designed to be switched on and off frequently, and there may also be a time delay between applying power and the lamp coming on.
I believe the enlarger uses a standard 24v lamp, but I'm not sure about the fan - do you know whether that's 24v or mains voltage? If the latter it would be fairly straightforward to rig up a separate mains supply to it.
Otherwise, your best bet is to keep the Chromegatrol power supply and as you suggest switch it to "focus", and get hold of a power relay with a mains voltage coil. Wire the relay contacts so as to switch the 24v to the lamp, and connect the relay coil to your Paterson timer. That way you'll keep all the functions of the Chromegatrol intact apart from the dodgy timer, and you won't cause any problems with its reliability or overheating. And of course you can replace the Paterson timer with a StopClock quite easily
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Hope that helps!