You should be just fine.

The reason that you glue the shear clamps proud is so that you have ample material to plane off when it is time to do the rolling bevels (page 105 of the manual).  The bevel is more pronounced in the center of the boat and really flattens out as you move towards the stern.  Since the angle is less on the stern, you don't need as much material so 1/8" should be fine.  Just make sure that you are a little less aggressive with trhe plane when you get to that area.

The only other concern comes on page 78-79 of the manual when you are leveling the hull.  If the shear clamp on one side is much higher that on the other, you will have to account for the difference so that you don't build twist into the hull.  This is not a huge concern because you are not building the space shuttle here, and 1/8" twist may not even be noticable.

   Thank you! That alleviates a lot of concern!

   You'll be fine.  The end result prior to deck installation is that the OUTER edge of the hull/sheer clamp need to form a nice "continuously straight" (no rapid up/down deviations) so that when the deck lays on there will be little to no gap along that OUTER edge.  So, when using your hand plane (recommended)/belt sander/sanding blocks to put the correct bevel on the sheer strake/hull panel, go for the correct amount of bevel, even if that means you never actually take any wood off of the inner edge of the strake in areas where you didn't leave enough proud.  And you can judiciously take a bit of extra wood off the outer edge of the hull panel if you think you need to in areas adjacent where you didn't leave enough proud sheer strake and blend that in to the overall longitudinal line of the hull panel, but I wouldn't recomend that as necessary, as it will make it that much harder to maintian that "continously straight" top deck curve with out having that perfect cnc-cut panel edge to use as a guide.  In doing all this there will probably be some areas with a slight gap along the INNER edge of the strake based on the way the deck curves down to meet the OUTER edge of the hull.  If it is clear where there will be a bit of a gap, just add a little more extra-thickened (non-runny) epoxy in those areas just prior to strapping/nailing down the deck.  Even if you end up with some areas of non-full contact along the inner edge, even if not filled with epoxy, you should have a stong enough overall deck/hull joint.  Do some dry-fitting of the deck to make sure things look good before you move on to doing the installation - that will probably take something like some ratchet straps.  And try to get some help with the deck install just to make sure you have sufficient working time to get things right, always important but maybe even more so in this case where your fit up might be less than perfect.

Thank you for taking the time to write that explanation! That really helps me visualize what's going to need to be done.