Thomas, you can shorten the big rudder if you need to and still get excellent performance. IMO, the big rudder is larger than it needs to be for all applications except AI sailing and boat wake rides.
I always use the large rudder, but don't hesitate to modify it for different applications. Here are a few, all of which work well for virtually all uses (except the one on the exteme left doesn't have enough authority for sailing):

Here's the drawing for another I made that you can see removed half the difference in height -- outstanding rudder! (note this was made from the old version of the large rudder, not the current model so the result is slightly different).

The sailing rudder has 90 sq. in., almost twice the 46 sq. in. of the standard rudder. Cropping 2 inches of your large rudder only removes about 5 sq. in. I think this would still give you excellent performance -- you probably wouldn't be able to tell the difference. By comparison, the one in the drawing here has about 66 sq. in. Of course, how the area is distributed is rather important.
In any event, I recommend you take your original standard rudder somewhere far away from your boat and leave it there!
