I installed the headers after the engine was already in the car. One only needs to raise the engine a few inches at the most. Can be done with a floor jack.
After my experience, I would frown on this. You have to be very careful not to dent the bottom of the pan. I did the same thing to mine (long story) and wound up with a pan that had a slight curve to it. I didnt think it was a big deal, but it could very well have gotten ugly/expensive quick. The pickup was rubbing on the bottom of the pan. On the other hand, my car is a previous generation Comet (65, column shift auto), but I dropped the engine in with the 88400s on and didnt have any problems.
I have done the same thing - with a floor jack as well as before I lowered the motor in (for the drivers side). The passenger is much easier! Even with a big block of wood? I've used a 2x6 square chunk many times with no problems yet. But I agree - be careful.
