if the bottle is leaking from the bottom (intake of pump) then there is no economical way of repair, epoxy etc will not stick to the PE material. You need a HOT repair with glas fibre and thermal set resin to repair it.
If your system is noisy and your high pressure line is not genuine Honda then forget about any repair. the original nylon braided line with built in valve is necessary to quieten the system.
BTW the pump cannot take in air unless the bottle is about 50% emtpy - its shape and installation location is designed as such to make sure no air enters the pump in any condition. When the low side is opened for repair, the manual suggests you hand spin the pump first with high side removed to make sure you remove major air from it.