Intake distribution issues

>As for the AG not being good on top, hang on;
even with 4.30s yur gonna be speeding at the top of Second Gear. And in first, as you know; it spins all the way thru. So what top are we talking about. lol.
I installed my AG waaaaay back in maybe 2001 or 2002 when they became available locally............ and I've never been sorry.
As for the air leaks at the header flange;
-If you got afterfires, you can bet you got fresh air in the exhaust
-if you got fire in the plenum , there's only one place it can come from which is past an intake valve. The how of it, you gotta figure out.
Your options are;
1) valves not closing, or not sealing, or something in the chamber, running hot enough to spontaneously ignite the fuel charge before the valve is closed, or as mentioned fire coming in during the overlap period.
2) As I think about it, this could also be due to bad cam-timing, but honestly if it was far enough out to be the cause, I doubt the engine would start. and
3) consider the Ignition timing. IDK how your EFI compensates for engine load. and if it doesn't then there is only one time the Ignition Timing can ever be right which would be at WOT, and over 3600 rpm. The entire rest of the time, the Ignition Timing would be retarded.
If the engine was running in such a mode, at Part Throttle, the mixture in the chamber, for a great deal of time is never gonna finish burning inside the chamber, and will have to finish up burning in the header pipes. and that means that the overlap period will be dead, for an instant loss of power. But, if the engine is simultaneously running rich, then the entire primary pipe, of every cylinder, could be filled with burning gasses. This is of course, very bad; cuz if the primary pipe ends up under pressure, when the exhaust valve next opens, and you have 61* of overlap, guess what; those higher pressure than what is in the intake plenum, are headed up to the plenum.
This is theory.
Does it happen in real life?
Well if your Sniper cannot add or subtract ignition timing in compensation for load, my guess is yes it can.

MY engine
which is very similar to yours, has up to 22* of Part Throttle load compensation, built into the distributor.

At idle, she is happy running at 25>35degrees. (but I only give her 14 max.)
By 2000/no load, she likes 40/45
By 2500/no load, she likes 50 to 55
By 2800 she wants 50 minimum, up to 60, just to cruise on.
But the Power Curve is 14*basic, >28*@2800 >34 by 3400.
These numbers produce cool-running in the Primaries and minimum fuel consumption.
Please tell me, the Sniper can control this.
If it cannot, you are gonna have to build your distributor with similar curves, and absolutely, you are gonna need Vacuum advance ..... and I prefer running it off the sparkport. If your sniper does not have a sparkport, (I wouldda never bought it) panic; the distributor can be made to work on full-time advance .