Modding is trial and error. I own and engine modding biz. We started out by modelling an OS V-Spec on high-end computers used in the Aerospace industry. But that was only part of it. Real-life testing was the next part. We learned alot...
Cutting the scoop will help some with packing. The flywheel (crank) is now lightened. Part of the affect of this is less low-end torque. If you are doing it to an engine like an RB, which IMO are already weak on the bottom it makes it more noticable... It will also spin more RPMs faster. We've seen con-rods go easily with this mod...
As you mod you may make the engine much for finicky when it comes to tuning. You make the tuning window much more narrow. Again, not good. There is a balance...
And as mentioned in one of the above posts, we is it you are looking to achieve? What is wrong with the current engine now that you don't like? Did you already try other methods to improve the performance such as different clutch shoes, pipe/header combos, plugs, shims?
Again, there is alot of work in modding an engine correctly. We've got a stack of destroyed motors from when we first started out...