Interesting.... replacing the A sweep start comparator has 'cleaned up' the end of the A sweep. Previously, when in ALT mode, there was a period approx half of a division at the end of A sweep that coincided with the intensity of the B sweep (as the beginning of A sweep does). This is now gone entirely.
Of course upon removing it, I checked it with DMM diode check and hFE and compared it against a NOS one and ones out of a 365 I use for parts. It appeared to be rather degraded but not entirely bad, but apparently not good enough for this circuit.
In order to determine whether or not my remaining sweep issues lie in the timing circuitry, I have decided to swap timing boards since there is only minor difference between the 00 and 01 revisions. Specifically in the A sweep high speed timing caps, which I have the parts to change over if I decide to keep it in.