340 rebuild,timing,intake manifold

If you had the cam gear set on 6:00 O'clock and the crank gear on 12 0'clock that is #1 exhaust TDC. You need to have both cam and crank gears set on 12 O'clock for it to be on tdc compression stroke. Everything else is right.

Note: Your valves may have been closed making it appear to be on compression stroke even though it was on exhaust stroke but that was probably because the lifters were bled down.