I solved my problem by installing the intake manifold and then distributor first and THEN doing the timing chain stuff. I put the dist in exactly the way I took it out and then was free to rotate the engine so the marks align at 6 and 12. Then I took the old gear off and put the new stuff on. BUT...with the marks at 6 and 12, the dist rotor points at the #6 cylinder position, NOT #1 telling me that the engine is set at TDC with #6 on compression, not #1 (#1 is at TDC, exhaust).
I'm not saying that engines were ever put together with the marks not aligning at 6 and 12 (I'm sure they were), but I am theorizing that there were some differences regarding whether #1 or #6 was set at TDC, compression. Even my own Haynes manual has a discrepancy - the text says #1 and the picture caption says #6.
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1976 Silver/Firethorn. L48, 4spd. Original 2 bolt, vortec heads, 9.4:1 CR, Speed Pro Cam: 224/224@0.050, 112 LSA, Eagle Steel Crank.