1) Can I place the car in "D" to prevent the diff from turning?
put it in park not drive to lock it up
2) Is there an inexpensive source for a new boot?
boot for what? on the tranny?
3) Can the rear diff cover be removed with the diff in place? May be necessary as the PO buggered the fill plug.
never tried, there may be enough there to get it out with a hammer and punch or chisel