Thankyou everyone for your comments, they've all been helpful.
I think I'll still try raise the bike back up, even if it doesn't help with the knee situation, as I didn't mention that I sometimes carry a pillion + luggage which means that the rear of the bike is riding incredibly low at times. The side-stand also hasn't been shortened so it can be rather precarious when I leave it parked up. In terms of getting the bike jacked up to swap the links out, I think I'll just stump up the money for the centre-stand as the rafter method isn't viable for me, besides at least it will make chain maintenance easier in the long-run!
I've checked underneath my seat and I can't find any indications whether it has been swapped out for a lower one or not. Unfortunately there's no part number markings other than "28K >PP< etched into the plastic. Any idea what this means? It looks like the beginning of the part numbers you mentioned, but crucially the identifiers that reveal whether it's lowered or standard are missing.