Arrrrgggg, looking at the schematic and the modification you are suggesting I would have to say be extremely cautious as you are bypassing a very important part, a fuse.
As you have draw the new red wire bypassing this 30 Amp fuse, the regulator is permanently connected across the 12 volt battery totally unprotected by a fuse.
So, if something were to go wrong with the regulator, either while your bike was on the road or sitting quietly in the garage, you would have a potential fire risk due to melting regulator, melting wires or worse still an exploding battery!
Please review your suggestion and consider replacing the existing wires with quality flexible wire with the capacity to handle the expected currents and make sure you continue to have the fuse in situation for your own protection as well as for your bike.
In my experience as an electronics / Industrial Controls Systems Engineer I would suggest that the problem you are describing and experiencing is not so much in the wire as it would be with bad connections, creating hot spots at these points due to higher resistance with high currents. The Regulator is trying to maintain a correct voltage and charging current to the battery, and if there is increased resistance as seen by the regulator it will try to increase the output voltage to compensate, thereby increasing the current in your feed to the battery. It can only go so high before the regulator and or stator decide to have a meltdown.
Check the cleanliness of all connections as well as for corrosion about the fuse, as dissimilar metals when in contact may cause corrosion.
Keep yourself and your bike safe, please keep the fuse in situation.