Water heat is fine. Its not like you are driving it as a daily driver. The intake needs a little heat to help with atomization. It will take the motor a few minutes of warm up to get to 180 where the therm opens and you are all set.
The stock set up is of course the better engineered set up and it plain works, as long as the butterfly is not frozen or the spring is not broken.
Running multi carbs, there is always a little trade off. I run the water to my Clifford 2X2 and the motor, with two Holley 2300 350 cfm carbs, runs fine.
On the other hand, if you are running or want to run a single carb, then use the stock exhaust manifold. You will be much happier. If you want, you can split the stock manifold.