A couple thoughts  before seeing the slips
1 - Bad SD, minor vac leak or something hurting it down low (I just don't ever see what you described)
2 - The late ICL of the stock cam was acting funky with the shorter runners
3 - The SD didn't like the Ford carb
However, after seeing the numbers
You are barely over 1% difference in speed and under 1/2% in 1/8 mile ET, and even the 60 foot is under 2%.  That seems to be that would be within the tolerance of measurement.
The last thing I may theorize is that the log manifolds take away any benefit of scavenging, which could require the longer runners to get back a little torque.  However, those numbers sure don't seem that different when looking at the spacer combo that does best
It's odd because I know you are thorough, but my 390 is light switch responsive with the baby cam and a 1 inch open and a SM, and even when it was a painfully deep quench low compression, it behaved very nicely.
As I think aloud, it could be the stock cam, RJP had similar behavior with his truck, and when he swapped to an iron intake got much better mileage.  Maybe the lack of overlap and late installed centerline with a stocker?
1. Could be, but this SM was pulled from a truck we had bought, was running fine. No data on that one, but it was running ok, no leaks of note.
2. I never really thought about that one, could be. I don't run many single planes. Back when they were new, I helped a friend put a SM on his 400M, stock cam, we didn't notice any issues with that. But again didn't clock it against any other intakes.
3. Again that could be - the 4300s tend to "get lean" at higher power and with open headers, but they usually don't complain thru iron manifolds and muffs.
4. One other factor I thought of is maybe the SM didn't like the mismatch to the larger b9ae-b intake head ports. The 428pi and 428cj intakes seem to like that mismatch, one of the things that makes the 428cj run good (else why would Ford use the bigger LR heads with the MR 428cj intake).
This car is pretty consistent - no wheelspin - the 3.00 gear is on purpose (and the big wagon actually is slightly TAIL heavy), so for me, .10 sec in the 1/8 mile, which is about .15 in the 1/4 mile,  is a LOT - I consistently rack those up as "wins". And you could feel it - where it was laying down compared to the 428pi, and then where it started to howl and get up and run.
That's why I suggested to the OP - just try both intakes! Sure its a set of gaskets but you learn so much. Intakes are SO unpredictable. Thanks for all the ideas. That mystery has bugged me for years,