Agree you have no real choice but to go aftermarket for the hydraulic top link. I have found the hyd top link to be extremely useful in all sorts of ways and recommend it highly. Would not even think of using a box scraper without one. Saves countless grief making adjustments and getting on/off the tractor. Works well with MANY if not all implements. Among the surprises is the assist it gives in hitching up 3pt attachments , being able to move heavy implements around a little bit without getting a hernia, etc. A nice feature is that they both pull and push.
Sort of alarming to hear that the tractor end of the hydraulic top link has to be ground down. There are world-wide standards for the 3pt hitch and somebody somewhere is NOT compliant with the standards. Either Kubota or the top link manufacturers, one. MtnView certainly sounds like he knows what he is talking about. I've only used the hyd top link on a larger MF tractor. If I were you I would get a caliper and make some very careful measurements of the 2650 top link connection space and then go shopping among the several manufacturers of hydraulic top links. A few phone calls seem to be in order to discuss the compatibility issue. I'd do quite a bit of that before doing any grinding.
I got mine through a very knowledgeable dealer who acquired the unit for me from a 3rd party. Price wise of course you are better on your own.
p.s.: Do some measurements on the length range you need for the top link. MtnView seems to have experience there and has given you a length range to look for. Take some measurements and see if that length range covers your applications. These things are not cheap (expect $500 or so) and you really want to get it right. I'm assuming without insulting your intel that you have the spare remote to use and all that.