This might be too late to be of assistance, Richard, but I have just faced (and solved) the same problem on my A Rap which I am rebuilding. My timing pinions are thankfully clearly marked but I wanted to check that the valve timings were correct before building up the rest of the engine. As you will be aware, the cams are not accessible once the cam box(es) are in place and trying to take a reliable lift reading with a dial gauge from the upper end of an unrestrained push rod is just not possible. However, if you wind a strip of paper round the upper end of the pushrod, securing it with a piece of adhesive tape when is of a size so that it is a sliding fit inside the pushrod tube, it will then slide up and down inside the pushrod tube rather like a piston in a cylinder. I then clamped the magnetic base of my dial gauge mount onto the top of the cylinder liner and was able to set up the dial gauge to take lift readings. Remember that the valve timings quoted are at 5 thou lift but, as Bob Stafford observed some years ago, do not expect the timings to accord with those given in the manuals. In my case, my Rap has 4X cams and while the inlet opening and closing and the exhaust closing values for both camshafts are near(ish) to spec, both the exhaust opening values are way out. However, on checking the figures on the Works Engine Build Sheet for my engine, I found that this was the case when the engine was first assembled! Hope this helps.
John