I made two new valves, this time using Ghosty's method of retaining them with an e-clip which is recessed into the top of the valve keeper for extra safety. I didn't make new valve cages and simply spent about 2 minutes per valve lapping them in with toothpaste. When I reassembled it there was absolutely zero compression turning it over by hand, which worried me until I noticed I hadn't installed the spark plug. Once the plug was in compression was quite good.
The crank didn't take much effort to press apart and I was able to determine that the shaft had spun in the web about 45 degrees. Not wanting to make a new crankshaft or web, I simply ran a heavy, coarse diamond knurl on the end of the shaft and pressed it back together with a liberal amount of 635 Loctite.
Once the Loctite had cured I attempted a start and it fired straight up and ran immediately. All up I've got about 10 minutes of running on it so far, but as Brian experienced I cannot keep the flywheel grubscrews tight (I built version 1 of the flywheel with the smaller hub and grubscrews before it was redesigned). While it was apart I machined a small dimple in the shaft for one of the grubscrews to locate into, so the flywheel doesn't walk off the shaft, but it makes a lot of rattles and clonks as it runs. I'm thinking I'll have to make up a new tight fitting custom key with a very slight taper on it which locks the flywheel in place, as per George Britnells' suggestion.
I'll also have to hunt down some sort of cooling fan and mount it up. The engine is such a great runner that I'm sure I'll be wanting to run it for extended periods which wouldn't be a good idea without some cooling. Plus, with all the power the thing has, I will have to construct something for it to actually drive at some point. With the open design of the engine frame, I'm thinking about maybe building a power take off driven from the cam or crank gears rather than a putting a pulley outboard of the flywheel.
Here's a fairly poor pic of the new valve retaining clip. The engine looks grotty as it was still warm from it's last run when I took the photo and I'm making sure it's well lubed up while it runs in.