I re read you post. Was it your intention to pull the drive out the top? That would be possible but not advisable for the reason the manual stated. Most improved (3/8") drives will not come out through the manifold anyway, the stock unit will but you'll lose the retainer clip into the
oil pan, not a big deal but not the best way to deal with the drive, as you must use a stock size drive and it may migrate up, losing
oil pressure (not likely, however possible)
The only right way to remove the drive is to remove the pan and the pump. I'd leave the old shaft in until you were planning on pulling the pump.