I am building the same rig.  I will watch this thread with interest. I used the smart track rudder system. I will use it for paddling as well.  I’m building a Mill Creek 16.5 and have just glued the top on. One final sanding and then I can fiberglass the top.  I went with the 55 spurred foot sail.

Be be careful as one thing leads to another. I just bought a lake home so I can sail!  It started with the Mill Creek, the sail rig, then I need a place to sail.   

 I too am building a sail rig - but in my case I'm pairing it with an WD12.  I have only started on the sail rig so far - but the instructions talk about adding a reinforceced hole in the deck for the mast, and a block that the bottom of the mast will sit on (both to secure it in place and for reinforcement).  You don't need to build them both at the same time.

I'm planning for sail on the smaller side, which should be plenty for a single kayak.  I'm sure you could sail your MC alone or with another adult, but the larger sail may be better if you think you'll have a buddy.

I think that the Mill Creek 16.5 with sail rig would be an awesome fun set up.  That combination has been on my list ever since finding CLC 10 years ago, and is still there.  I have purchased the sail rig plans but have not finalized which boat to put it on.  A MC16.5, BootLegger or our Shearwater Double.    

My biggest input is regarding the rudder.  The Smart Track will absolutely be inadequate for a kayak equipped with the sail rig.  First, if you read this article, John says so.  (https://www.clcboats.com/life-of-boats-blog/kayak-sail-fun-evolution-of-a-kayak-sailing-rig.html).  Secondly, if you do some research you will find that generally speaking, rudder size should be 1-2% of sail area.  The largest Smart Track blade measures approx 10" long with ~3" chord, giving it about 30 in^2 surface area, which equals 0.21 ft^2.  That is about 1/10 the area required depending upon which sail you choose.  The last issue is waves.  With only 10" below the waterline, it does not take much of a wave to lift the rudder clear.  I have the Smart Track rudders on four kayaks and find that over 2' I start to loose the rudder.  Picture shows the three Smart Track blades on the left.

My other input is sail size.  I beleive that 40 ft^2 sail is too small for that boat with sail rig.  If you go that small, skip the sail rig (amas) and go with the Mill Creek Sail kit which has a 39 ft^2 lug.  It is far cheaper and a lot less work.  If you want the sail rig with amas, go with the 70 because you can always reef down.  

That’s good to know the smart track rudder is too small. I ordered the tiller style rudder when I ordered my sail rig kit but changed my mind. I’ll have to see what I can rig up.  Maybe just build a bigger rudder.   

Sorry to say, but I do not think that making a bigger rudder to fit the Smart Track will work.  First picture shows the largest Smart Track blade (double) laid on top of the plans for the CLC Sailing Rig Rudder.  My rough math is that the CLC is rudder is at least four times larger.  Even if you were able to enlarge that blade that much, I doubt that the aluminum rudder housing will handle that much load.

 Another problem with trying to use the toe controlled system is that your rudder throw is limited.  The toe controls only move a couple of inches so you only get around 30 degrees max rudder deflection.  That works fine for kayaks but even with a larger rudder will be problematic trying to tack or jibe in some conditions.

I do not know what your sailing skills are, but as a lifelong sailor and former US Navy sailing instructor, I will tell you that sailing a boat with too little rudder is challenging.  If you are a beginner, trying to do so will be counter-productive.

If it were my build, I would either remove the Smart Track system or modify the boat now so that you can use either rudder system.  It will be much less work to fix it now than to wait until you have it all glassed and varnished. 

As a last note, if you are intent on modifying the Smart Track system, you may try keeping the rudder head and building a larger rudder around the lower blade.  The picture below shoes something similar where I had a custom weedless rudder built for my race boats.  DK cut down a standard ST blade, then glued a CF weedless blade over the top.

   So the smart track aside. There are two rudders offered with the sai rig. Tiller or foot operated, are the blades on these two the same size?

Thanks for your help PP

   My sailrig plans only show one rudder blade, the one pictured above.

I had all the hardware installed and the cables run in my kayak.  The smart track has way more than 30 degrees of steering.  I made a new rudder blade from a cutting board of HDPE plastic. I won’t be able to retract it from the cockpit, but that’s not a big deal.  We’ll see how it works when I finish the sail rig and when the water in MN softens up a bit.