Any ways to put an ejection seats to the new Cockpit?

That will eject the whole cockpit lol @TweedleAerospace

Also make the interstage and engine the same Ag so that they activate at the same time. You only need a little bit of power and burn time.

Yes. Make a small fuel tank and attach the cockpit to it. Then rotate it until it is upright. Then attach a motor and a side interstage to the bottom. Then you can attach it to the whole thing by the interstage.