A little more info here:
https://rennlist.com/forums/996-forum/1124013-996-3-4l-and-986s-3-2l-differences.html
According to Byprodriver, who built a few upgraded engines, the heads & cams are the same - That would be with the exception on the mounting for the intake. If you are using the 986 S intake and head, that is not an issue.
I trust Byprodriver - He hasn't logged on the forum for over 6 months, but he'd be a great source for the build if he answers a message.