Stuart,
The triple row chain is not as fussy as the belt. My method is to assemble the stepped washer over the new clip on the transmission shaft (recess towards the tranny), then replace the shims that were removed (or if it's a scratch built I start with one .036" ). Slide the clutch drum and engine sprocket over the shafts (no chain) and with a hollow drift (I use a piece of aluminum tube) tap the engine sprocket until fully seated.
With a straight edge across the face of the teeth of the engine sprocket, measure the distance from the clutch teeth to the straight edge. Remove the sprockets, add the appropriate additional shims behind the clutch drum and re-assemble with the chain. Re-check the measurement. The shims are available in .036" and .048" thickness. I have found that most of the time, one of each is required, but not always.