I've got a gas water heater in a mobile home. Fresh air comes in to the water heater "closet" via a pipe coming from underneath the mobile. A while ago the heater was replaced, I'm guessing not by a licensed plumber. The combustion gases vent is no longer vertical - it leans at a little angle, and the fresh air supply vent is aligned almost exactly with the air intake vent on the heater. We've had complaints about the burner (or maybe pilot light) getting blown out, and now that I'm here looking at it, windy conditions outside seem to be related to the burner not burning evenly. (When I watched it on a windy day I was concerned the burner might get blown out, as whole sections of flame were gone (oh, 25 degree angle of no flame).

I have not had anything blown out (assuming by wind), but haven't had extremely strong winds in the 9 days I've been here.

So, is my assumption that the combustion air intake of the heater should NOT be precisely aligned with the outside air supply correct? (In other words, do I need to move the water heater back to where the exhaust ( B ) vent aligns with the rest of the exhaust system, as well as rotate heater so fresh air vents aren't aligned)?

open some windows on the home, leave the water heater closet door open and cover the fresh air intake in the floor.
see what happens?
BTW, i've never seen this problem before.
all the problems i see are related to not enough make up air or gas pressure not set correctly or burner gas/air ratio not correct.
lastly, a big word of caution here. gas is very dangerous.