The pump is in the front of the gear box, it is driven by the back of the converter housing. I cant find a picture of the of it, but it looks like it uses a spline instead of two lugs to drive it.
The way to fit the box is to put the converter in the front of the box turn till it engages the drive shaft, then turn some more to engage the pump drive shaft.
Offer the box up to the back of the motor and locate spigot on the front of the converter into the hole in the center of the flex plate. The box should slide in and you should be able to turn the converter as Lee says to line up the flex plate bolts.
It looks like the converter has moved forward during your struggles, to disengage the pump splines. You need to loosen the bolts between the engine and gear box, to let the converter turn, take out the flex plate to converter bolts and turn the converter around till it does engage properly.
With a bit of luck nothing will be damaged.
Harvey.
