2006 RSMV loss of acceleration

[Melk]

Good afternoon, 

I have recently gotten my bike running again after sitting a couple months and replacing the battery and regulator. I’m now having issues with loss of acceleration. I can still ride around town no problem with 1st thru 3rd gears (lower power output), but it’s still not what it use to be before I had parked it. 4th and 5th gear are basically nonexistent at the moment. I can use them with very little power in those gears. I audible did a small re-sync on the carbs and it has helped it some along with running seafoam thru the tank. Any suggestions would be helpful as for the local Yamaha tech is wanting to charge $500+ to look into the matter. 
Thank you. 

[luvmy40]

Drain the fuel tank and refill with good gas. If it sat for any length of time with ethanol in the fuel, it's garbage.

Check/replace the fuel filter.

Verify the fuel pump is working.

Do a compression test.

Synchronize the carburetors with a four channel manometer.

Have the valve shims ever been adjusted?

How many miles on the clock?