FIXED Strange Misfire on New Engine

This is a weird issue for me that I have not seen.  2001 Chevy Silverado 2500HD 8.1L.  This engine uses the regular old LS1 PCM and 1x/24x CMP/CKP.  The customer rebuilt the engine himself and upon installation and initial fire up, it has a random misfire code (P0300 is the only code) which per the customer was NOT present when removing the engine for rebuild (rebuild done for rod knock, still ran well with no CEL per customer). Misfire counter shows on cylinders 1,8,3 only. The firing order is 1-8-7-2-6-5-4-3 so notice the 3-1-8 misfires are sequential.

Any and all input would be appreciated...

CUSTOMER BUILD INFO (all this is initial parts / work at the time of build, no diag / swapping of parts done by customer before bringing to me for the misfire issue)
- Full Long Block Rebuild, heads, pistons, rings, bearings, "RV" cam (it is bigger than stock but small for an 8.1), crank, and even a new engine block and intake manifold.
- Customer installed NEW genuine GM CMP 
- Customer installed Cloyes timing chain/gear set, not chineeseum junk
- Customer moved OEM reluctors from OEM crank to replacement crank (crank had destroyed rod journal requiring replacement)
- Customer installed NEW Standard Motor Products CKP (this concerns me a little not being OEM)
- Customer installed NEW injectors

DIAG DONE
- Swap any of these around (Coil, Plug, Plug Wire, Injector) and the misfire doesn't move
- Compression Good at 160 +/- 2 psi across the board
- Leakdown Good across the board
- STRANGE - Unplug a plug wire on a non-misfiring cylinder and then it will read a misfire on the unplugged cylinder BUT one of the others (1,8,3) will STOP misfiring!
- Since the misfire moves when unplugging an initially "good" cylinder plug wire and the "bad" one corrects and ceases the misfire, I am relatively confident this is in the ignition side and not fuel or mechanical.
- Cylinder 8 misfire count is roughly 30% higher than cylinders 1 and 3 which are about equal
- Firing order on cam card checked and the card claims it to be correct
- Customer says he used a degree wheel when he installed the cam and camshaft timing was dead on with the cam card
- Injectortor test will fire all injectors and they all end up within 0.5 psi rail pressure of each other

The attached scope image is back probing PCM at CKP and CMP and an inductive lead on the #1 plug wire for the trigger.  Blue is the inductive trigger on #1 plug wire. Green is CKP.  Yellow is CMP. 

For comparison, I found a sample of the expected 24x CKP pulse (on the LSEngineDIY site) and how it should look in relation the 1x cam pulse.  To my eye this looks like what we have.

SCOPE PIC ATTACHED

Anyone have any ideas?

Thanks.

Two different ignition systems were used with this ymm. If you're dealing with a distribuitor I would have a VERY close look at the ditribuitor cap. They were known to cause a LOT of trouble back in their time.
(That's where I would put my money at...)

On a non original cams the firing order may change due to a different arrangement of the lobes. Although typically this change inverts the firing for the cylinders 4 and 3 with the cylinders 7 and 2 nevertheless It may be worth to assure that the applied firing order truly is the correct one for your cam. You always could check wether ignitin takes place close to TDC compression.

What does a secondary ignition capture show?

Thanks for the reply.  This is NOT a distributor style ignition, it is an LS1 style Coil Near Plug.  The cam card shows it has the original firing order, not the old BBC order. I also checked the cam part number to confirm. I suppose it is possible that the cam was ground wrong but I think that is pretty unlikely. In my scope pic, you can see that the #1 firing event is quite a bit advanced from the falling edge of the CMP which leads me to believe there is a significant ignition timing issue going on where the spark is way too far advanced. Since that is not adjustable and the CMP and  CKP signal appear to be in proper sync, I am not sure what could cause that to be so far out of whack.  I found this image on the LS1Tech website (see attached) that shows what is supposed to be the proper relationship of these signals and it looks like my CMP is a few degrees retarded relative to CKP but the #1 firing event is SIGNIFICANTLY advanced. Since this is PCM controlled I am not sure what would cause such a huge variance if the CMP and CKP are in spec, which they appear to be.

Would you have a true secondary capture of a good and a misfiring cylinder with a capacative probe on the plug wire instead of the sync probe's signal?

That is an inductive clamp on the plug wire. It is as accurately representative of the plug firing as a timing light and I set it as the trigger channel for time reference on the other channels so it should be what you are looking for.  I scaled it with a caliper and it looks to be 69 degrees of ignition advance at 1,500 RPM. Doubtful the advance is causing misfires on 3 cylinders but perhaps whatever is causing the misfires is causing excessive advance??

A secondary capture with a capacitive probe on the plug wire which I asked for will show show more critical information as firing KV, burn time.... Two captures from a good vs a misfiring cylinder allow direct comparison.

Applying degree rulers to a capture with coil activations within one complete engine cycle will show where each cylinder is firing with regards to TDC compression. Could be by coil currents for example. I doubt commanded spark timing would change that dramatically and fast on specific cylinders.

Problem found.  We did not know this but the customer re-loomed his injector and coil harnesses because the stock loom was rotted. He did a good job and it looked OEM.  HOWEVER, when he did the job, he re-applied the OEM cylinder number decals on the coil ends so we thought it was OEM and did not verify the routing.  Turns out that he mixed up cylinders 1 and 3 on one harness and 6 and 8 on the other. Back probing at each coil and comparing coil pulse to compression it was obvious the timing was off on those 4 cylinders and the other 4 were perfect. Swapped them around and it runs like a top.  Still not sure why it had 3 cylinders misfiring instead of 4 as it should have or why the misfire moved around when unplugging good cylinders but that will be a thought experiment for the future unless someone has an idea as to why that would have been happening.

Nice work, thank you for posting the fix

Thank you for the feedback. Another lesson on man-made problems.