Thanks. Since that y hose goes to the evaporative system, it narrowed it down enough for me to get it going. It's running well now. I put 50 miles on it ranging from around 25-65 mph.
It makes a rattling/ticking noise only while idling and with any throttling the sound goes away. I don't think that noise was there when I test ran it with no exhaust/panels installed.
I wasn't expecting a knock - I adjusted the valve clearance to the manual specs, and checked oil level. The crankshaft bearing seemed solid, without any play. I wonder above all, can it be serious if the noise is only there when idling?