Timing V12 engine in '72 series III

I just bought a 1972 series III, V12. It ran rough, but it ran, when I got it. Exhaust had a sort of tootley popping note that sounded odd, but since I'd never one one before...

Went to set up the notorious Zenith-Stromberg carbs, and obeyed the instructions of setting the timing first. I could not get the timing to match the 4? ATDC spec at idle (w/o vacuum retard connected) or to the 12? BTDC static spec. Did the best I could with that, set up the carbs per the books, but the exhaust still sounded funny. Today at the NJ Jag picnic (had to drive an Audi to get there) I heard a proper V12 exhaust, and mine is nothing like it.

Verified the plug wires were in the right order (beware the Chilton short guide--it showns the distributor turning backwards compared to what's marked on the distributor cap!). Then I took the cap off and noted that when the crankshaft is at the 12? BTDC static mark, the tick mark on the magnetic timing disc was at 11 o'clock, pointing to the 1A cylinder lead, NOT to the pick-up unit at 6 o'clock as shown in the official shop manual. Removed the distributor, aligned it to match shop manual specs and drawings. Now the engine won't start at all, and as a bonus, it spits smoke out of a little hole on the side of the left rear carburetor. I suspect the whole engine is slightly out of synch, but before going to the next step, is there something I'm missing here?

Alan