Hi San Bernard,

You seem to have the general approach down so let me break down your questions and address each part:

1. Do I rough up the area of overlap on the hull?  It should be sanded….and appear hazy.  It does not need to be aggressively roughed up. You certainly do not want to be so aggressive that you cut back into the glass.   A light sanding with 150 to 200 grit will do the trick and ensure a good bond.
2. Do I apply epoxy just up to the edge of the tape trying not to involve much of the tape leaving the un-epoxied cloth hanging over?  Just over the tape is all you need but I would not overthink it or try to be too precise.  I usually use 1 inch blue tape when I perform this operation (its easy to see when you have started to involve the tape)….and I typically go a ¼ inch to ½ inch onto it….but if I go more its no big deal.  The tape and any epoxy and glass over the tape is coming off so you are balancing neatness/wastage with speed of operation.
3. When the epoxy gets rubbery do I cut/score the glass at the  toe of the tape then pull off?   Yes, just cut slightly above the blue tape top edge and pull off the tape and the glass/epoxy over it will come with it.   The most important thing is a good sharp blade and being attentive to cutting it when it is ‘rubbery’.   This is the step that it is important to stick around and monitor it.  Not rubbery enough and you will see it move under the blade as you cut.   if you stick a gloved finger on it and epoxy comes off….you need to wait…but once a touch test shows it has set up….start your work.   no more than 30 minutes between tests as you get close.  If you get distracted and step away for a couple hours at the wrong time….you will have a mess. 
4.  I don't want to cut into the existing hull glass in the process, any suggestions on how?    When the time is right, score no harder that you need to make the cut.   a sharp blade will help minimize the pressure to cut the rubbery glass/epoxy.   I also pull the tape away as I am cutting to confirm that my cut was adequate.  Of course, ensure the layer below is fully cured.

 I hope this was helpful.  You can also set up a test on a scrap piece of wood if you want a little practice on how it is done.

h

while its not an MC 16.5 ....here are two pictures of the process i am describing above.

the first picture if the blue tape in place and glass applied on the deck mating it to the hull:

and the next picture is a couple hours later after it was rubbery and the cut has been performed, then allowed to fully cure and then feathered with a small sanding block.

while there is a bit of a line viewable in this picture (had not completed the feathering) it was totally invisible when it was completely finished.

h

   Wow, just what I was needing to clear up the questions that I think about at 3am. Great response along with pictures of your beautiful build. This Forum has really helped me with my project, many thanks to all the "ambassadors" of wooden kayak builders out there! SB