For now you should be able to run with the rear port to manifold vacuum and leave the front open. Don't cap it or pressure can build up from heat or the movement of the main diaphragm. That should act like driving without the EGR active.
The EGR adds a little extra pull to the modulator. When the EGR opens the engine has less vacuum but not extra torque. That loss of vacuum at cruise would normally make the transmission go into a later, firmer shift. So to keep the transmission shifting correctly with the EGR open a larger, secondary, diaphragm is used to help the main one. A booster to the modulator for when running the EGR.
If you were to Y the 2 ports you would have very early and soft shifts. The transmission would be adjusting for very low torque inputs even under moderate loads. There is a good chance you could get the transmission to start slipping and burn it up. Bad idea. The single port is a pretty foolproof way of going conventional. If you are stuck running around with that dual port, let that front, large diaphragm breath freely and just use the standard port.