Towards the end of the film, Nitro seems to be spending most of his time rewiring the entire radio system. A large job like that would ideally be done in a refit alongside a quay wall. Given how Nitro looked to be busy rewiring everything else during that time, it's likely Graham gave Dodge too little time to fully refit the Stingray to put him at a further disadvantage during the wargame.
During the climax, Captain Dodge calls to the engine room and tells MMC(Ret) Howard to "Give me everything you got!" Howard pulls out a bottle of whiskey, takes a swig and dumps the rest into the fuel tank, telling the men in the engine room that it will thin out the mix and give them a higher RPM rate. Normally, such alcohol would be forbidden on a commissioned Naval vessel. However, (1) Howard is a retired so given a bit of leeway, and (2) they were told "think like a pirate." Classic pirates are famous for having alcohol onboard their ships.
This is actually something you can do with pre-TDI diesel engines, although you can expect to have to do a rebuild shortly after as it will damage the gaskets.
Also, just because alcohol is forbidden on a US Navy ship doesn't mean crew members don't have any. They will just get in a huge amount of trouble if it is found.
