A centre stand is still way the best way to support the bike to do this and you're right about the footrest shoulder bolts holding the forward mounting holes of the centre stand brackets.
Just take the footrest hangers off on the side or paddock stand and then substitute the forward stand bolts for normal M10 bolts or put the shoulder bolts back in naked.
I had one mounted on an SS which doesn't even have footrest hangers nor shoulder bolts and standard bolts worked fine.
Just don't put too long a bolt in as it could puncture the crankcases!!
I've got a couple of the bolts used on the ST2/4. M10 x 20 I think.
Urgent edit.. Don't take the shoulder bolts out with the bike on the side stand as one holds the side stand too.
You must put an M10 back in the side stand too or it will swivel round and the bike will fall over.. Ask not how I know.