Rebuild Runs Rough

They say,and I don't know the truth of it, that Q from .050 to .080 can be more susceptible to detonation than any other Q. But that's for a gas-burner. At .085 and E-85 I imagine you should be fine, especially with smoothed chambers.

I think, think, that late closing intake might be a bit of stinker to tune in batch.I'll be watching to see how this plays out, so I can learn too. You might need a higher than normal idle speed to start off with,IDK.......

Yeah I’m thinking the crank trigger may be at fault. It seemed a little eccentric on the pickup when setting the gap. Maybe play with the noise filter. Surely something is making it run poorly. With so many changes, I just pray it isn’t anything engine mechanical. From the compression test, I really don’t think so
he magnetic pick up should not care about a few thousands runout, so long as the gap does not become excessive, so as to not be read at all or to be inconsistently read. The Moparmagnetic pick-ups that I have tested are good to at least .028 gap.

Because that cam has only a small amount of overlap(possibly as little as 40*), and because you are not running a tuned exhaust, it seems to me you could
install the cam at quite a bit advanced, to close that intake a lot sooner. You said in an early post that it was in on a 113 ICA, and I grossed your .050 specs up by 52* to get an idea of where the intake was actually closing, which got me an ICA og 68*. IMA thinking you could advance her up to 6 or 8 more degrees. This would increase your cylinder pressure as well.
From this;
Static compression ratio of 8.62:1.
Effective stroke is 2.47 inches.
Your dynamic compression ratio is 6.68:1 .
Your dynamic cranking pressure is 97.76 PSI.
V/P (Volume to Pressure Index) is 71

to this at 8 more degrees
Static compression ratio of 8.95:1.
Effective stroke is 2.66 inches.
Your dynamic compression ratio is 7.38:1 .
Your dynamic cranking pressure is 115.31 PSI.
V/P (Volume to Pressure Index) is 90

Don't look at the numbers as absolutes cuz we already know they don't match up to your engine. Rather look at the percent increase ; from 98 to 115 is about plus 17%, and changes the ICA from 113 to 105.
That might be excessive, IDK, but 4* would certainly be do-able: here it is at 4 more degrees, 109 ICL
Static compression ratio of 8.95:1.
Effective stroke is 2.57 inches.
Your dynamic compression ratio is 7.16:1 .
Your dynamic cranking pressure is 109.75 PSI.
V/P (Volume to Pressure Index) is 83
now an increase of 12% pressure, and an ICA of 64*

I am speculating that the earlier closing intake would help clean up the intake, increase your intake vacuum,stabilize the idle, and increase your off-boost torque. But there is no free lunch. To get the extra compression degrees, using the same cam,it has to be stolen from the power cycle; so losing 4,6 or 8 degrees from 108 is gonna cost you a bit of off-boost fuel economy.