A simple hardware modification to disconnect the JVS controller from port 0 (port A on the Dreamcast). You just need solder jumper JP3 and switch it. This is a very useful for DreamShell and running games by it.
After this, you can connect all Dreamcast peripherals to port A. This will result in three ports available on the side board: A, B, and C. Port D is not routed on it, but may be available on the motherboard connector.

You need to find it on your revision of motherboard. The jumper pads is present on all NAOMI revisions. Here I will show an example on the most common version:





Here is the route that needs to be cut:


Like this:


Soldered jumper:


And switch this jumper to the second position:




Thanks MetalliC and Tchan for this info.