While mine isn't a 400F, I went the route of no-return modification. My XS650, and your 400F are not so rare that I'd be overly concerned with keeping all the tabs etc. intact. Lots of room for some modified bikes out there. Mine was in pretty poor shape. 1972 frame (which as the first XS650 design frame might have had some intrinsic value as they redesigned it the next year) with a 1978 engine that had zero compression. It wasn't doing me any favours, but I think I greatly improved on it.
I sold off the tank, sidecovers, seat and ears to someone who wanted to restore one. Covered 80% of what I paid for the bike. The only bits I've used from the original bike are the frame and engine.
Note how clean the frame looks with no rear footpeg mounts, no tabs for sidecovers, battery boxes, fenders etc. etc. etc. Not trying to persuade you - if you're going all-out and are intending to hide electrics etc, then chop away. If you're going to leave most of the fundamentals in place, then don't cut anything off.
BTW - once I cut off all the bits from the frame, I could comfortably walk around with it in one hand. Didn't weigh it before and after, but I must have cut 30 pounds off it.
My XS650 before (March 2007):
And as of Sunday March 23 2008: