Wow, that does change things a bit. The pertronix system isn't that sensitive to changes in distance between the pickup and reluctor magnet as far as I know, so even in a worn housing they are usually more accurate than points. I'm going to shoot in the dark a bit now. Timing light, is it a set back type? If so it might be variying a bit electronically. I have seen a loose ring on a harmonic damper before but that's really a reach so don't put much faith in that being the cause. I will assume that you got a new rotor and cap with that new distributor, perhaps the rotor/cap gap is changing enough to cause the spark to be delayed a bit, again a bit of a reach, but the new distributor really takes away a lot of the more likely causes. Try unhooking the vacuum advance line and pluging that just for grins, that might cause a bit of spark scatter. Let us know what you find, it's a real interesting problem.
'73 Midget (V6)
'59 MGA (I6) under construction
'73 Lotus Europa
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