Removing the Weber stacks could reduce the air flow through the carbs by as much as 15%. The Weber stacks are especially efficient at getting the air to smoothly flow into the carb. Just take one off and look at the ugly hole that is left. If you are really close for space shorten them or if they are late model Webers then they are the bolt on air horns and there are some after market horns that are very short.
Rex
I do a LOT of Weber flow testing. 15% is too much, BUT, expect to lose a solid 6/8% of FLOW. AND, turbulent air in the carb may cost more in terms of hp.
In addition to the above comments, taking off the stacks will change the harmonic tuning of the pipes which can affect the power and power curve. On my engine a 1 inch difference in stack length moved power curve 500 rpm. Your comment about the engineers is of course appropriate, but other features of the engine and its use affect the required length. And what you want to know is total length stack to valve and the rpm range you run in or want. A shorter length moves tuned curve up generally speaking. And the actual point of tune is approx. 1/2 stack diameter above the physical end of the pipe so if you are pushing the tune take that into consideration with your calculations.
I had similar concerns about the distance from the box wall to the stack and though it is hard to figure without either dyno testing or CFD or someone with lots of experience ( I used the latter mostly) and aimed at at least 1 diameter of the stack from the wall over it. Your 2" is probably adequate. ( see above 1/2 stack diameter comment). Much of the air flowing into the stack is coming from the sides anyway, not straight down. As I recall airbox volume is recommended as being at least 2x engine displacement. Lots of varied opinions on that one.
Flow steal from adjacent firing cylinders does happen. Not sure how much it may affect things. Would need something like 02 sensors in each pipe, careful plug reading, etc to try to see and then possibly tune each cylinder( if possible) to compensate. I have seen a flat plate inserted between the stacks to try to fix this. Personally probably wouldn't go there without surely proving its necessity (and a power improvement therefrom).
Weber engineers provided differing stack lengths for the reason of tuning.
My experience (ymmv) is that there is little "charge robbing" in independent runner systems, as long as the distance between stacks is 1 x the stack diameter, or more.
Velocity stacks not only provide an optimally smooth path for the air to enter the carburetor, they are also a tuning device for the inlet tract. By adjusting the length of the stack, the harmonics of the inlet tract can be matched to the desired operating rpm of the engine. That is why various length horns are available--some pretty short and some rather long. You definitely do not want to simply delete them.
A 2” clearance at the end of the stack should not make any noticable difference in performance.
Absolutely YES to all of the above! Again clearance should be 1 x diameter MINIMUM. 1.5 x d, or 2 x d is better, but space is always at a premium . . . . .
Sometimes Most times little things have consequences - intended or not!
Does paying attention to all the "little details" matter? I dunno, but I think you should ask the guy who finished second . . . . . Fordboy