I'd leave it until after the deck is on.  The excess thickened epoxy that will squish out when you attach the deck will fill those spots.  Just make sure you level it off at the hull/deck joint before it sets too much so that you save yourself some sanding later.

Cgris

thanks for the help

And when you're finished attaching the deck, roll the hull over so it is upside down.  Then the squished out thickened epoxy will tend to flow back into the seam all along the outside of the hull.  Makes for an easier clean up later.  An hour or so after you roll the hull stick your head into the cockpit cutout (carefully) and look for any drips running inwards from the sheer clamps.  Clean any you see.

I think you should stick with your original strategy of filling in the low spots on the sheer. I think some of the respondents misinterpreted your post and seem to think that you want to attach the deck while the thickened epox is still wet.

If you are nailing on the deck, the nails will force the deck to follow the shape of the unfair sheer clamp. You could even get low spots inboard of the sheer, depending on how severe the low spots are. You won't be able to fix any low spots on the sheer after the deck is attached and an unfair sheer line is very noticable.

Fill in any low spots with epoxy/sawdust and let the mixture cure. Then sand the fix with a fairing board until you get a fair sheer line. Then attach the deck.