For us in the forum world to try and help such as this of us not knowing much regarding your specific marine technician's fuel injection experience capabilities, what engine models he's used to seeing on the daily basis of using his preferred fuel injected scan software for in-depth sensor output testing, reading, etc., Rinda is an often preferred marine scan tool to recommend that most anyone would be able to buy such as boat owners themselves, new or old boat technician's, dealers, etc., to help narrow down a lot of EFI engine diagnostics issues as it's easier to use outside of being specifically trained to use a specific engine branded; dealer capable software/computer connected to factory scan tool system that often needs updating via a internet connection and password protected.
Here's the (an) easy to use Rinda scan tool typically referenced online,
https://www.rinda.com/techmatepro/index.html
There are a slight few other marine scan systems out there too it's just sort of hard to know on our end if what your marine tech is using might help with your engine brand problems is all being he seems to do diesel stuff which could be a wide variety of engine brands that may or may not pick up on your Mercruiser engine 496 MPI/555 PCM correctly...Again it's us not knowing his knowledge evident of your mention the boat has also been to a certified mercruiser dealer in the past that couldn't seem to help all that much themselves for the time spent on your engine.
Though sort of hard to theories on this as to why exactly as you'd think it'd be an idle RPM only issue, The IAC on a 496 MPI has been known to do some real odd things to this engines performance wise and warning horn wise at all RPM ranges plus it's been known to melt the IAC's wire connector harness and/or have an internal PCM failure of the IAC circuit as it's a motor driven 12 volt system...Not the 5 volt system of sensors.
That mentioned regarding the IAC, it sounds like you've been mostly all through it and it don't seem to be the case any longer and probably is the case here, 'Though you can't/haven't and shouldn't rule/d it out completely just yet, 'Like the Rinda scan tool does there may be a test feature within your service tech's software that could try preforming an IAC output test to see if it helps does anything to help know if you should continue down the IAC's path or not before heading elsewhere.
Fully remove, check and reinsert (all) the fuses for the IAC circuit.
Also you mentioned the tech is testing high RPM's while not under load and only able to get to 2400? RPM...Though you may be seeing something there not in gear under load because it's seems about the same as you recalled being on the water doing the same, please just be aware that not testing under load you may not find or notice the exact same lost performance symptoms as other possible normal working sensor features could be duplicating your true performance issues such as like over revving and the rev limiter holding the RPM down.
^ Sometimes the shift actuation switch might think the gear is in neutral gear even though you are in forward gear and the PCM sees that and if so you should be able to read that on the scan tool used as you shift through the gears.
One thought to maybe consider trying if at all possible would be to try your thought to be bad PCM on a known good running engine of the same year, model, fuel design system as your engine is to see if the good engine stays running correctly with your PCM....But don't put a good/someone else known good PCM on your engine in case something on your engine is causing damage to the PCM.
I can sort of see where Whipple can only be vague with their responses as they ask that before sending the PCM in you do the best diagnostics as possible and from there they know what to inspect from past experience of visual and multimeter testing, etc. as they have done/repaired many over the years now. Though I don't know if they keep a in-depth paper trail of what they tested/repaired exactly for each unit that comes in the door?
If they didn't see anything wrong then at this point you can only run with the assumption the PCM ought to be alright and something on the engine is bad unless you can try the PCM on another engine to satisfy the theory better.
