Not sure what rudder you're talking about but the non vertical stern was an issue for me mounting a sailing rudder so I modified it this way.

https://www.imagevenue.com/ME13H5OC

PP

To my eye, the MC has a pretty pinted bow and stern, so I think it will track just fine without a rudder.  Looking through the pictures that CLC has posted, I note that something <25% of the boats shown have rudders, and many of those have sails. 

If you are not going to sail, I'd suggest delaying the rudder install until after you paddle the boat.  It will be easy enough to retrofit after.

Now for your questions:

1.  Through bolts with backing plates or washers would be the best way to attach the rudder mount.  If that is not possible, then definately either an end pour or hardwood inner stem.

2.  Looks to me like it would fit, but you may not be able to use the aft bolt on top.  Another option is to cut the stern square after installing the deck and doing an end pour.

3.  A micro balloon endpour should be sufficeintly strong.  That is what I use in my boats to save weight.  If the end pour is very big, it can cause heat damage to the boat exterior.  Either do multiple small pours or have the stern in a bucket of cold water when you do it.

4.  Personally, I find the mounting bracket ugly.  I prefer to install a bayonet sleeve into the stern of the boat.  CLC does not sell this part, but Stellar US does (Stellar Kayaks USA, L.L.C. :: Steering :: Bayonet Pin Sleeve).  If you go this route, you need either an end pour or inner stem, and a relatively square stern.  You also must buy a rudder housing designed to lock into the bayonet sleeve.  Picture below shows the bayonet sleeve in my Yukon and Mystery.  I intentionally posted a LARGE picture so that you can zoom in.