Regarding some points raised about practice times:  I see no reason why 250s couldn't go out with the rest of the classes for practice.  They do at the Manx.  To say they'd be in the way is, I believe, a perceived problem, rather than a real one.  I was talking to a (recently) ex-TT 250 rider and he says he used to get held up through the twisties by Superbikes as he was carrying much more corner speed.  

The Le Mans 24 hour car race accomodates cars of very different performance levels.  You might have a Porsche 911GT3 doing 180mph down the Mulsanne Straight being caught by a prototype doing 220-230mph.  They don't seem to have a problem with this and they have do it at night!

I concede that accomodating the 125s in practice presents a bit of a challenge, so how about ditching the rookie lap on the first night of practice - I've never met a rider that likes it or thinks it's useful - and give an hour of that session over to the strokers.  The rest of the session can be used as normal - it's untimed after all.  Following that the post race practice sessions that no-one really bothers with could be given over to the 125s and they could have their race on Friday morning with the Senior to follow.

Of course, all this depends on getting a worthwhile entry for both classes but does it sound like a plan?