'03 Yamaha 250 HPDI trouble

[nogoyamaha]

I bought this motor used 2-1/2 years ago and have been having trouble ever since. I have been a Yamaha person all of my life, but this motor has me doubting any other yamaha motors! I have changed 10 micro filters, cleaned the injectors, changed the VST filter, the fuel strainer, the secondary filter, changed all of the hoses from the tank to the high pressure fuel pump and running from a remote fuel tank and my motor does the dreaded "bucking" as the HPDI's do. It runs good for the first few minutes then it starts bucking and will eventually shut down, but will crank right up after a few seconds. I removed my primer bulb and ran the fuel line direct from the tank to the motor and it still does the same thing. I tested the fuel pressure on the medium pressure pump and i'm getting 48 psi.
What can i do to get this motor running?
I'm ready to junk the motor!

[99yam40]

Monitor fuel pressures while problem shows up.
Computer hooked up will help as the HP side is very high and there is not a place to hook a gauge to even if you found one to read that high.
And th computer will show lots of other info

[nogoyamaha]

I'm a do it yourself person, I guess from here i will have to bring it in to a shop for further diagnostics? If so thanks for your advice!

[rodbolt17]

if your such a backyardigan, why not simply monitor the voltage on the high pressure fuel sensor?
the spec is right there in your service manual.
does not take a computer to monitor anything on that motor.
every sensor on that motor can be tested with a standard voltmeter.
yes the laptop is faster and eaiser, its just not mandatory.

[ausnoelm]

I can't believe you have tinkered with this for over two years!