Toss-up on a very difficult decision: No. 1 I think is the seat mods.
Improving the atrocious OEM Honda seat was mandatory and fundamental to me, because I don't think my wife or I would have ridden the ST1300 for long unless we were comfy and confident. The John Moorhouse seat put me closer to the ground so I wasn't always on tippy-toes, gave me long-distance capability, and stopped my pillion sliding forward under brakes.
I had it covered in leather, and after many many kilometres, i had it recovered. I brought this seat with me to my second ST1300 (swapping it over).
A close second is the communications gear. Initially, on my first ST1300, I had J&M gear, which provided for 27meg 2-way, rider to pillion, feed-in from Honda radio and Zumo MP3 - brilliant. Now my Starcom does it even better with less bulk and digital.
Whilst No.2 is brilliant, I wouldn't be riding the ST without No.1.