If it's worse with the air filter on I would look for a blockage somewhere along the pipes, it's probably something stupid like a rag being left in a port when you were having it re-ground. Put in to stop Swarf getting in and overlooked on the rebuild.
Just be methodical and keep your temper, it's only a lump of metal after all, no malice or ill intentions, although I wonder sometimes.
That's my twopennorth anyway, good luck.