During distributor replacement, I followed timing instructions to the letter from many posts here. For the life of me, I cannot get the timing 1000 rpm (with grey spout connector removed) to the spec 5 degrees BTDC. It running at about 10-12 degrees. Anything lower and engine gets rough and then dies about 6 degrees. 

My questions:

1) I feel like the outer ring on the harmonic balancer has possibly slipped over the years. It was not replaced during rebuild. Engine is likely timed correctly but appears off due to slippage. If this is the case, this would mean engine is not externally balanced correctly. How big of a deal is this and can it damage anything?

2) I am aware of Damper Doctor (and the other company Dudes). I am considering shipping mine down. But does anyone have a GT40 handy that they could align the 4 bolts into a cross and tell me where the spike aligns to on the outer wheel (or any other orientation you think makes sense). I'd love to compare to a working one and see if it is obvious its slipped an by how much approx.

3) The casting part number is F3JL-BA. I have searched high and low and cannot find a referene to this this HB online anywhere, even ebay. 

Any other ideas on the timing?

JQ

Mark the balancer again.   There will be a distance between the two marks you make.   The center point between your marks is true top dead center.  TDC.   This mark should match the factory line on your harmonic balancer for TDC.   If it does not match something has changed, maybe wrong balancer installed at the rebuild?

A piston stop is just a tool that screws into the #1 spark plug hole and reaches down into the cylinder so you can set a stop very close to TDC to do this measurement.   Many retailers sell them including Amazon.

Here's a picture of a 351w harmonic balancer used on the marine 351w engines. 

This one is a 3 bolt balancer but that doesn't matter. 3 or 4 bolts, the keyway and the TDC mark will be the same in the boat application

The long scribe mark at the lower left is lined up with the center of the keyway.

The short scribe mark is lined up with the TDC mark on the outer circumference.

Measuring along the outer circumference the distance is about 2.16 inches or in degrees the TDC mark is about 39 degrees to the right of the center of the keyway if you have a timing tape for a 6.375 inch diameter pulley.

This is for a 6.375 inch diameter balancer which yours is, with the timing pointer at about the 1 o'clock position on the timing cover which yours is on a gt40

A balancer for a 351 w with the pointer in a different location like on many automotive applications would have the TDC mark in a different spot.

You'd probably get good accurate numbers if you did all this with the balancer off the engine, but being a mid engine boat, if you take the lower pulley and the crankshaft bolt off off and get in the right twisted and contorted position you could get some decent measurements.