Very ODD indeed!
I Don't think I have ever heard of a BANK of plugs going out and the other working fine..(assuming you checked 2,4,6 and 8 for fire, not just 2...)EVEN with one set of points firing, it should hit on all 8...
Try running a battery jumper cable from the battery , insert the spark plug BODY into the other clamp put on each plug wire and look for spark ... (you can hold it in your hand without getting bit this way *AND* you have a Bonded ground without having to "Just get it close to the block..!)
TRY running a Ground strap (or jumper Cable) to the passenger head from battery ground..and see if spark returns, maybe the head is insulated by gaskets and sealers and the change of the manifold sealed (pun intended) the right head's fate as to a proper ground bond..
One other thing , It may be possible that in changing the manifold, you may have dropped Or rested the manifold (or other heavy part) on the plug wires for the passenger bank..and internally cut the cores..Try new wires or swap in some known good ones.
Other than that, unless you have a Crossfire cap..I can't think of anything that would effect plugs 2,4,6 and 8 in a row..since the FO (Assuming SBC) is : 1,*8*, *4*, 3, *6*,5,7,*2*..It (the Dizzy) would have to do a lot "OF SKIPPING around to miss the four in a row..(astric's are passenger bank)...
Keep us updated..