Anybody know how much different the exhaust holes going through the transom need to be on a tall deck setup versus a short deck?

No one else seems to have an answer for you. So I will tell you that it is approximately less than .5 inch taller and wider. My boat has had both and the headers and tails fit with both short and tall. Probably a way that you can fudge without major changes. Really not a lot of difference. Hope it helps.

It really depends on what pipes you have. The shorter they are, the harder it is to make them fit. The collector will move out about 3/8" and up about 3/8". That is assuming you are using the same heads. Some heads have raised exhaust ports. They can be raised as much as .600"
Eddie

When you say shorter, are you referring to the distance between the end of the collector and the transom?

Do Dart Pro1 heads have the raised exhaust ports?

Dart Pro 1's are raised .300

Yes, that is what I'm refering to. The shorter that the tailpipe is in length, from the collector to the transom, the harder it is to make adjustments.
As mentioned, Dart Pro 1's do have raised ports.
Eddie