I managed to get my engine in the frame tonight. I fitted the carb to see what the clearance to the shock was like. Seems pretty good. But I had a quick measure up of the manifold anyway. On the front left corner of the carb, there is only 4mm gap to the manifold. So a shorter manifold, or one that kicked the carb more to the left would not be practical. (This is on the standard KX500 manifold)
One issue I didn't forsee. There isn't enough clearance to fit fit the clutch cover with the engine in the frame. So I'll have to remove the engine bolts and tilt the engine forward to get it on.
Once again, if somebody can suggest which airbox boot to use???