Bike sat for a year, now it wont run well

Looking for some advice / support.
I have a 2008 wr250r that was running well, was put in storage for a year and now starts fine but doesn't appear to be running well.

Symptoms: Bike is starved for fuel, It appears that the programmer/ ECU isn't moving between zones correctly which makes me now think one of my sensors is not functioning correctly.
However, the previous owner removed the stock dash and replaced it with a trail tech unit. This has made debugging incredibly difficult. As such, if there is anyone here that could spare to loan out a dash unit for me to see if I have any codes stored that would be fantastic. Have no issue paying a deposit and shipping both ways. Or if someone is local to the SF Bay Area I could come and grab it. I have tried the Yamaha FI diagnostics tool meant for motorcycles, but it appears to have a different communication protocol.

Mods:
- Thumper Racing big bore kit
- AIS delete
- EJK programmer
- Safari Tank
- Replaced fuel pump 2 years ago


Symptoms/ issues fixed so far:

1) Initially the bike was not starting at all, I tracked this down to what appeared to be a bad pressure regulator on the fuel pump, this was replaced and the bike would now start
2) filled tank with fresh gas
3) Bike still ran poorly: replaced the nylon fuel line between pump and injector: hose was permanently deformed/ pinched
4) Cleaned injector (flushed with solvent and injector cleaner)
5) repaired the vacuum line coming off of the injector which originally went to the AIS (This was definitely cracked but is 100% fixed now)
6) Played with every single setting in the EJK programmer. Some settings work better than others but can never get to full RPMs

Any help would be appreciated

Can you elaborate on what the exact problem is? You say it's starved for fuel, but how did you arrive at that conclusion? IOW, how does the problem manifest?

The OEM display is helpful, but you can still do a lot of troubleshooting without it: go to Page 8-71 of the service manual and start checking all the components described there for proper operation.

You should pay particular attention to the Air Intake Pressure Sensor: you need to do a complete sweep of vacuum vs output voltage to determine whether the sensor is good.

In addition to the above, you should:

1. Replace spark plug (unless you recently did so)
2. Check for proper compression with a pressure gauge
3. Check for correct fuel pressure with a fuel pressure gauge