Just cut the guides down a bit, it will help more than hurt as long as you smoothen it out after you cut it down
How do you adjust your readings to the ambient air density?. "Technically", because the air is actually getting pushed, not pulled, ("technically", there is no power called suck) the air density can make a big difference. I would think that the device you are using to produce a vacuum would be affected by air density also.
Orifice plate type flow benches are self correcting by nature. As the ambient air density changes your test pressure changes. But since you are correcting your flow reading to a standardized test pressure, generally 28", you are automatically compensating for any difference in ambient conditions.
Can you please send me the pictures of your flow bench? I'm building a bench and am looking g for ideas.Technically it doesn't matter, a given volume of air through a given orifice size will produce a given pressure differential,doesn't matter if the air is being pushed through or pulled through. Realistically though it would be better to do it closer to the head, if they're are any leaks in the system it will read those too, so the closer you have your meter to the head the less room there is for leaks to be introduced. If you want send me a PM with your email address and I can send you some pictures of the inside of my flow bench, might help to clear some things up and see how things are set up.