As a last resort, I'd take the u-joint apart and use a gear puller on the (now accessable) yoke. That way, no loads are transmitted to the tractor's drivetrain like when prying.
edit:
If you don't have a gear puller, you could put a shaft thru both yoke holes where the cross-bearing used to be. Drill and tap a cross hole thru the shaft for a bolt to tighten against the end of the tractor stub shaft. A lot of thase stub shafts have a center drilled hole so if your bolt had a point ground on it, it wouldn't walk when you tighten it.