Re: Shorten / hem a special hakama: opinions.
I think the run of the mill "Ask your sensei" fits perfectly well here. I would ask, and I bet the reasonable answer would be yes.
As for tailoring it, perhaps seek out your previous tailor.
Personally, if I were given permission, I would hem it myself. Very slowly. Very carefully.
It's your aikido, passed on to you from your teacher, from his teacher. Your shihonage is not that of his teacher, neither is it wholly like your teacher's. It was made by you from what you received.