When a problem developes after a prolonged storage, my first thought is "stale gas" or water in the gas. Have you done anything to combat "skunky gas"?
Are there any Check engine DTC codes? Any blinking check engine lights? If so, please post the full codes. Most any local autoparts store will read the codes for free.
How did you clean the MAF? The MAF is easily damaged by harsh cleaners. Clean with a product that does not leave a residue.
The post states the misfire goes away above 2500 RPM's. One possibility that comes to mind is excessive EGR flow.
A vacuum leak can also cause the symptom listed. Note, even a tiny vacuum leak can cause problems. This can not be over emphasized.
Partially clogged injectors are another possibility (poor low flow spray pattern). Confirm that the fuel pressure reference line is connected and leak free.
Do you have an ODB2 scanner?
FWIIW, do not disconnect the COP while the motor is running. This will generate a continious misfire with the full unburnt fuel charge going straight into the exhaust. Once in the Cats, it will flare and overheat the cats.
If an injector problem is suspected, consider an injector cleaning/flow testing service such as injectorrx.com. Cheaper than new. Once tested, the injectors are as good as new.