Thats what I do. Drop the flex plate bolts and pull the box with converter fitted. When putting the box back in, I push the converter into the box and support its weight while I rotate it to make sure I can see and feel it locate and drop into the oil pump drive in my th350 boxes. The cutouts for the oil pump drive in the torque converter tube are quite deep. When the box is fitted I pull the converter towards the engine about 3-4mm to make the converter lugs meet the flex plate as this is the expansion gap that you should have.I've always believed you take the TC out with the box, so looks like you need to re-mount it and make sure you re-fill it to the right level. Did it dump any fluid when you pulled it?