Ignition/spark question

[roccit_53 at scirocco.cs.uoguelph.ca (C Boyko)]

Okay, I'm just fishing in case someone strikes on something that works. I'm
trying to figure out why my MkI has gone from starting and idling to
running on one cylinder (number three in particular). Spark seems to be the
issue. I drove the car on CIS with Megasquirt controlling spark and it did
a marvellous job (so the map is good, and it functions), and this revised
frankenbuild started and idled well on both fuel and spark, until I got a
throttle cable and was in a position to actually drive it. It has not run
on all four since. I've done some basic diagnostics, Dan has been very
helpful on the MS end of it, but it appears that only one plug is firing
with any regularity, based on clipping the timing light over the various
wires. Many of the components are either new or have been swapped for
different ones with no improvements. What I guess I want to find out is
what the causes of a no spark could be. Plugs wouldn't go bad all at once
with the car sitting (they are new), nor would plug wires, or the cap or
the rotor, but tell me you oddball tales of queer spark behavior.
New components include: plugs, wires, cap, rotor, and obviously MS and the
wires to Hall, power, ground, and coil associated with it.
Swapped components include: coil (tried two), and ignition distributor
(broke one and replaced it). The fact that I do get spark indicates that
basic function of Hall and coil are okay, but what if the coil is weak? I
just reinstalled the firmware, so corruption there isn't the likely cause.

Anyway, fire it at me, I thrive on the confusion. Thanks. 
cathy