The flush port is actually inline with the jet pump supply line, it just follows gravity and heads straight downwards out the jet.
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10 minute ENGINE RUNNING FLUSH or ENGINE NOT RUNNING FLUSH? Does your manual specify "ENGINE RUNNING"? I think it must not specify? Regardless, if engine block cooling jacket is not filled with water, cylinder sleeves will overheat. :O !!!
I think the current method is not being interpreted correctly or there is something unclear about the instruction from the manual.
I'm not a sportjet guy so I'm thinking in terms of an outboard engine. There's always an air vent at the top of the block. This is the tell-tale "pisser" outlet. When water is coming from this vent, the block cooling jacket is filled with water. In this case, it's safe to run.
Under any circumstances if no water is confirmed coming out from this air vent at top of block, "pisser" I'd say the block will not be cooled. For an outboard, we look to see if water is exiting the pisser at all times and if not, we investigate the cause (usually the seawater pump is not working). The sportjet receives it's cooling water from the jet pump, that is the primary difference between it and an outboard.
So for 10 minutes of flushing while running the engine, you must devise some way of connecting such that the engine block cooling jacket is kept filled with water. Perhaps use a high pressure fire hose, or alternatively by connecting somewhere else?
Facts are facts, poorly written or interpreted instruction manual method doesn't change them. Bean counters don't care much about these details until after the fact when it comes back to bite them (Yamaha has won the majority outboard market).