Intermittnet HPDI issues

[Pig Pen 250]

I have a 2003 250 HPDI that I am having some issues with. Sometimes when I put the throttle down to get up on plane, I can only get 3800 to 4000 rpms. If I throttle back to about 3/4 it runs weak. If I put it to full throttle, it sounds like its missing. Then sometimes all of the sudden as I'm going along, it will kick in and seem to run fine and I will get up to 5800 rpms..

This past weekend after I launched my boat, it was acting up and I ran about 30 miles and then all of the sudden, it kicked in and ran.

Sometimes when I start it , i get excessive smoke.......I have had the oil recal done.

My top end is at 46 mph and before I was getting a solid 52 and up to 54 mph.

Something just isn't right...any ideas would be appreciated.

One other thing that I had forgot to post earlier was that I'm also having issues putting the motor into gear from neutral. sometimes it locks up and wont let me put it into forward. I put it into reverse and then back into forward. It can take several tries to get it to go into forward. I am wondering if this could be causing a problem with the shift position switch. Due to the lack of top end speed, intermittent rpms from 4000 to 5800 and excessive smoking at idle sometimes.

Thanks

[rodbolt17]

shift position nor shift cut have any affect on N to F or N to R.
only from an ingear to N shift.
test fuel rail pressures at the failure RPM and load.
check the shift linkage,especially directly below the throttle body,for debris or loose bolts.
keep running an HPDI especially a 3.3L when its running poorly and you may get to post about detonated pistons.