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Should the jackshaft have any noticable end float? There's no mention of it in any manual. Mine moves about 11 thou which seems a lot. If you have to shim the crankshaft sprocket to line it up with the jackshaft sprocket it seems pointless if the jackshaft moves. My retainer plate shows some wear but I don't know if the groove in the shaft is also wearing. The rear of the jackshaft sprocket is also worn suggesting the endfloat is not a good thing. Thinking of getting a thicker retaining plate made to reduce the end float but don't want to stop it moving if it should do. Trying to stop a knocking/tapping noise inside the front cover and this seems like the most likely culprit.

The jack shaft doesn't get much load in axial direction, the only function of the retainer plate is to keep the jack shaft in place and reduce movement and thus load on the timing chain.
So how much is "11 thou" in normal (metric) measurements and compared to the space that the sprocket has inside the timing chain?

"11 thou " (.28mm) is starting to get a bit much I would have thought, as to weather or not it is causing the noise is hard to say, about 4 to 8 thou would be about factory spec I would think, I see there is no setting in the w/shop manual, maybe try a new plate first and see if it is a bit thicker but be care-full having one made as the wrong hardness of the metal will either wear the jackshaft or the plate.
Have you checked the water pump bearings and drive? if the bearings are tight that may cause extra load on the plate and possible wear on the plate and drive gears any excess play could be transmitting through to the front cover.
Another thing to possibly check is that the cam buckets can wear on the outside dia. where they run in the head but this makes more of a tappet noise like excess valve clearance.