Replace it.
Unless you have a repair person who has plenty of experience with that exact transmission....then pay him to fix it.
Have been into plenty of them myself and there have been times when I've put as much money into it (in the form of labor + parts) that it was cheaper to just replace the unit. But occasionally an owner is dead set on repairing as opposed to replacing.
When you said you had the pump head machined, what exactly was done? I guess I don't follow. Do you mean that the wear area of the HST rotating group was scored and subsequently machined smooth? If so....that's not the correct way. Why? Now the carefully designes clearance between the rotating group and the port block assembly is lengthened-which WILL cause issues. Besides, if that part is scored, it's junk and it's very likely that the clearance between the pistons and their bores are also loose which also causes problems.
Also....did ya put the check ball back in above the filter assembly? Hydrogear doesn't even tell you where it goes. Nor does Kubota since Kubota's manual is basically copies of the Hydrogear book. So if it falls out, you better know where it goes. If not back in the right spot, you'll have problems. BTDT.