At 2500 its also is jerking and plugs are black. As soon as it gets to 2800 it smooths out.
Can you watch your timing with a strobe when this is happening? Free revving you should be around 25°-28° at this rpm and approaching 30°-32° by 3-3.5K rpm.
I have 27 degrees of advanced and timing is -24 at 3500
This is way too low (assuming 24° BTDC) for just free revving w/out a load. It would be a safe area to be when making boost @ 3500rpm and up. Let the MSD6 BTM handle that. Set your full advance to 30-32° BTDC @ 3500rpm and turn the knob on the BTM to somewhere just under 1°/lb of boost. So by the time you reach ~13psi boost pressure, your timing is down around 24°. If the distributor advances a total of 27° from idle to ~3500, you need to do something to limit it's advance travel or get a different distributor. Don't set your idle timing super low just to keep the total advance within reason. You only need about 20° mechanical advance from the distributor.
Do you know your base fuel pressure, accurately? The 50 idles should be fine, 200 airs might be causing your rich in transition problem, but you've got to get your timing dialed first.