Once you put the dual 38's on it I would think the recomended specs for mounting to a stock twin carb 701 as listed on the Factory Pipe site in the instructions sections should get you close. Read there disclaimers carefully and consider starting "fatter" to start with just to be safe.
Only two variables in your setup are the case style and whatever minor difference there may be between the "Dry pipe" and the "Freeride Dry pipe"
I think it's just an issue of ECWI or not between the two pipes . . . . . the Freeride pipe being the one without ECWI . . . . .
In theory the case style shouldn't make any difference. . . . . the fuel/air requirements of the cylinder are based on port timing and area. . . . but, the increased intake tract length and less efficeint flow characteristics of the 61x cases may result in some of the charge remaining in the cases due to a less efficient secondary opening of the reeds. This would require a slightly richer mixture on the 61x cases to obtain equal performance with the same cylinder on 62t cases. . . .
Download this page :
http://www.groupk.com/tec-carbs97.htm and read it over and over and over again untill it starts to make sense to you . . . this way when you go to the lake and your ski acts a certain way you will remember what the symptoms mean.
Take a copy of it with you too . . . and make notes of your changes and the results you got by making that change.
Mikuni has a really good carb tuning guide but I couldn't find it after a quick search . . . . you might want to take a couple of minutes on your own it's worth looking for.
Good luck with the project. . . . . .