Thanks for the insight gents. I think maybe I figured something out over the weekend. While I was lapping the valves I kept finding that the the suction tool was pulling off the valve face. I wondered if this may have been caused by one of (or both) of the following - 1. the face of the valve wasn't smooth enough and 2. the lapping compound was too thick. So I took one of the two valves that we were leaking (the other 14 were sealing just fine) and ran the face over the brass wheel on my grinder. Then I added a small amount of WD40 to the polishing compound - that worked a charm.
I think what was happening is that the thickness of the compound (it's also pretty cold still in my garage) was preventing me from being able to grind the compound down enough while lapping the valve, as the suction tool would pop off before it got thin enough. By adding the oil, it lubricated the lap more and therefore the lapping compound broke down completely. When I reinstalled the two valves that had been leaking before and filled the port with acetone guess what...no leaks.
With the valves installed I moved on to the forks. To anyone reading this that hasn't disassembled these forks before it's a really easy job with the right tools -
but (as I found out on my last CB750) a right pain in the arse without them. The good news is, the right tools turn out to be not too many tools at all. Once you've got the oil and long spring out (there are two springs in there), clamp the lower tube in your vise. There's a 6mm allen bolt at the bottom of the lower fork tube - chances are you won't be able to remove it as it's bolted to a stem that sits underneath the long spring (in the bottom of the lower tube). Turning the bolt will just spin that stem. Here's where the other tool comes in - a broom. Shove the broom down the upper tube and put pressure on that stem sitting in the lower tube. With pressure on the stem you can then engage the allen bolt and unscrew it. For the visually motivated (like me) -
Remove the fork from the vise, and tip out the stem (there will be a smaller spring on this stem too - if it doesn't come out with the stem then it'll be stuck (loosely) on the bottom of the lower tube, easily removed). Then you can remove the dust seal, the large circlip (I use a couple of mechanic's picks to get that out), and slide the upper tube in a kind of slidehammer motion to ease out the fork seal. Job's a good'un.