There is a frame section under the drivers feet / firewall area, jack stands will be fine there, just put them on the straight / flat area.

It is OK to jack the car up from the front cross member also.

For the rear I regularly jack the car up from the differential then place jack stands under the lifting pads. I have a set of old time thick pipe stands that I've made a new adjuster for using a 3" diameter washer ( Ford truck radius arm washer ) and pipe. The allows the washer to capture the pad.

I'd go with pulling everything as a unit. When I removed the trans ( 722.6 ) from my 97 C280 is was a tight squeeze to the the bell housing bolts out.