Just like has been stated here, the larger stroke will give more cubic inches and optimize the cylinder head flow at a lower rpm, and make more torque (power down low.) This is what you want for your application. When someone says that a certain engine breaks, I really gotta wonder. It is the same exact parts with the width of a McDonalds straw more stroke. Unless it was the crank that failed, the blame cannot be placed on the cubic inches. I have built at least 10 engines this year with a 4.25 stroke or more and yet to see a single failure due to stroke increase.
Yes, lots of us racers go with a shorter stroke for a few reasons. #1 is cubic inch limits or weight breaks for our class. #2 some vehicles don't like down low torque, so we cut the stroke and make the power up high without unsettling the chassis, or boat.
But one thing we need to look at with the 3.76 stroke and 4.25. The short stroke will make power higher in the rpm band with the same heads. But you are puting unwanted strain and wear on the valvetrain to do so. The valvetrain does not know the cubic inch. The less you have to spin it to make the desired power, the longer it will live. And the lower the rpm's, the less we can spend on valvetrain and get away with it. Cuz let me tell you, I can run a 565 to 9,000 rpm's all day long. But it is going to cost more in just valvetrain upgrade than your entire build x4.
I say put the stroke in it and make your power down low.
The best place on the planet to get cranks, rods, etc is Dyno-Flo in NV. Dyno-flo.com Check every price on the planet and they will be the best bar none. I don't have 15 posts yet so I cannot post a link.
And don't worry about the clearancing. That is easy stuff.
Good luck with the build. Sounds like it could really be cool.