Wild, wild, wild guesses:
-- Throttle isn't being fully advanced (disconnect throttle cable at throttle arm and advance by hand to check at injector pump to check)
-- Fuel shut-off lever isn't all the way down, restricting fuel (check to make sure it it all the way down, hold it down while testing to check)
-- RPMs are being measured inaccurately (Check with a ~$20 phototach from amazon. Be sure ratio is set right at gauge. If using phototach, be sure to check at dampener, not at alternator or water pump)
-- There is a fuel supply or return problem (often also shows very prominent RPM surging or tons of white smoke or slicking at higher throttle settings). Are all valves open (supply and return)? Filters clean ? Lines in good condition(not delaminated or clogged)? Is the low-pressure lift pump pumping well (crack a line to test)?)
-- High RPM setting on pump governor is not correct (maybe try adjusting it and see if it improves -- without surging, smoking badly, etc. See below.)
There isn't really enough information to diagnose this...let's try working through it.
Which perkins 6.354 do you have? Which injector pump? The engine serial number is right by the injection pump in the block. if you are at the side of the engine looking a tthe pump, it is just closer to you than the pump. Can you post a picture of the tag on the pump? Between the two, the expected behavior might be clearer.
How long have you had the boat? How long has it been exhibiting this symptoms? Is there one engine or two? If two, is the problem on one, or the other, or both?
Are there any other symptoms? Surging or uneven RPMs? /Excessive/ white smoke? /Excessive/ black smoke? Blue smoke? Excessive slicking of the water? Hard to start? Leaking fuel? Stalling?
How are you measuring RPM? If you are reading from gauges, just to make sure we are playing fair, try with a phototach. They are ~$20 from amazon. To get the best readings the easiest, I like to paint the dampener black before putting on the reflector, but in most cases, this isn't necessary. Just be sure to measure at the dampener, not at the alternator, water pump, etc, because they are different sized pulleys, so the ratio means that the RPMs measured at places other than the dampener will be off by a multiplier.
In many cases the controls are constrained, either by intention, or by physical constraints, or by old cables. You do want to make sure you have verified close to full range or are testing at the pump. It isn't unusual to limit the controls a bit so that they can't damage the throttle arm assembly.
The pump does have a governor that limits high RPM. As I remember it, the adjustment screw is in (unsurprisingly) the governor housing, right near the idle RPM adjustment screw. The idle RPM adjustment screw is the an easy landmark to find, because it is the one on the outside of the governor housing with a spring on it, a slotted head, and the textured sides. It is very obviously intended to be adjusted.
If you find the idle RPM adjustment screw, the high RPM adjustment screw is right next to it, but within the governor housing, so not directly visible from the outside. Instead it is recessed a bit and covered by a rubber plug, which is in turn held in place by a small l-shaped bracket that can be seen from the outside. So, basically what you'll see is the idle adjustment screw and then, nearby, a ~3/4" bracket held down by one screw on one side and poking into a hole on the other side.
To adjust the high RPM, you unscrew the screw holding the bracket, remove the bracket and remove the plug. You can then put a screwdriver into the hole and adjust the high RPM screw. As I remember it, it is a small slotted screw and vert small adjustments make very large differences. So, //if// the problem is a misadjustment of the high RPM limit, this is where that would be adjusted. Once done, just reinstall the plug and the bracket that holds it. It is obviously helpful to vary carefully and precisely note the original position, both for reference and to be able to go back to it. Remember: Tiny adjustments.
I'm nowhere near my boat and have no documentation on this, so take it with a grain of salt. But, it is from memory and should help you find it.
I think the basic idea should be to sort out what the expected behavior should be, be sure of what the current behavior is, cure any other problems, i.e. surging or shutoff lever or control, then try adjusting the high RPM setting on the governor as a last resort, i.e. when it is clear that the engine is freely getting supplied good fuel and is easily able to return it, is running well without undue smoke or surging, and is showing no signs of leaks or other problems (the only issue really is the high RPM, and it has been isolated to the high RPM)