Differences between side draft manifolds?

[Whizbang]

im going to go uncover my short runner manifold and give it a look over. From previous examination, i think it could use some work with a Dremel to optimize it. But i think ill attempt to do a comparison between manifolds.

Now what im not sure about is HOW to do it properly. When the manifolds get swapped, i feel as though i might have issues with having the carb tuned properly. At the same time, i want conditions to be similar. so i might have to do the runs on different days due to the tuning and wait for similar temp and humidly days.