Convoy behaviour is hardcoded, nothing Core can change.
The naval buid program represents the ships and the tech level the Soviet Union had at this time, Stalin did not really focus on a nay but on Army and air force.
If you're running out of coal/energy you probably have built too much factories consuming all of them, you traded away too much of them or you failed to research proper industry techs increasing resource output.
The soviet Navy should not have generals but Admirals..... maybe they start without naval leaders and get them later. They may also have been killed via the purges.