Tank,
You might wish to send Mr or Mrs WeCVO a message some dealerships won't change any part of the build and demand it go back to stock when they rebuild it other dealers will allow you to swap out parts.
I think before you go much further I would have a very candid talk with the dealership service manager and see where they are will to let you bend the rules of the warranty and go from there. I think then you will be better armed to decide what you would like to have done to this motor. After 2 motors one would think they might let you be in the driver seat, so before you spend a lot of time I would check out your do's and don'ts and come back and tell us what your mind set is based on talking to the Stealer SM. If you can make changes do you have a fund setup for how much you might be willing to throw in of your own money, it might help decide what you wanna do.
My question to you would be what do you have in mind that you want out of the bike you obviously want reliability, more power? ,more torque? If so where do you ride and where do you want the power .... low end, top end ?
Some Suggestions:
Once it is covered by warranty whether it be the whole motor deal or the bottom end depending what was blown up I would buy a new steel SE Crank for the difference and send it off to falcion or dark horse and have it balanced and sleeved or welded depending on your preference. 1 likes to weld them 1 likes to sleeve them.
I would then look at the next weakest part the shoe cam tensioners I would consider upgrading them to gear drive or looking into the 07 style cam plate oil pump etc or just go to the fueling lifters, cam plate and oil pump and go gear drive since the crank would have been done. Cost of the Crank being done is somewhere between 450-650 dollars depending on who sends it etc.
Beyond that it is up to you whether you are going to want to stay stock or go for some power improvements besides say the 575 cams fueling lifters, pump and plate is a good ocmbo if your just looking for some better oomph without going crazy. Then there is headwork or uping the compression or going to 107 top end or a 113 motor since the bottom end is going to be taken out of the bike it is a perfect time to go this route and you can get very good numbers without having to go crazy in the build as Sir Mikey103/sir mikey 113 did although I think Tommy0 now owns the bike and it was 121/117 with 103+ heads and SE 251 cam (07) 50mm throttlebody or >. He swapped the heads out of the kit that the 113 came with and opted for the 103+ heads.
My suggestion would be to go to the 113 with the 251, roller rockers, Adjustable pushrods, and if they will let you put in Fueling lifters and oil pump and leave it alone there that way you should have a dealer that will stand behind ya and it should be reliable and you will have plenty of power when ever you want it, and send out the crank to ensure it is balanced etc.
Best of luck with this crappy situation,