OH NO! Sorry to hear man, yeah you cannot stab an AUTO tranny like a CLUTCH. 2 very different animals. This is 100% the problem.
The converter must be inserted into the trans and alligned with the front pump.
With trans out of car, Carefully put the converter over the input shaft and push towards tranny, then slowly spin converter while at the same time pushing in. Once aligned correctly you will hear/see a very appearent THUNK when the converter sinks into place. (this may take a few complete rotations to finally sink down in the trans)
Then you can raise the transmission into place, align the alignment dowels into the bellhousing and then start putting in bellhousing bolts.
Once all bell housing bolts are in and tight the converter should spin freely with your fingers. This is when now you can align the torque converter/flex plate bolts.
The Torque converter will be able to move 1/4-1/2 inch forward towards the flexplate freely for aligning torque converter bolt holes.
You will prob only be able to get to 1 maybe 2 at a time. So align the converter up with the flexplate bolt hole(s), then install and finger tighten the first torque converter bolt. Rotate the engine 1/4 or so by the front crankshaft bolt to expose the next flexplate bolt hole and then again align and finger tighten the next torque converter bolt. Repete this till all converter bolts are in and finger tight. Then once more by rotating the engine 1/4 turn at a time tighten up all the torque conveter bolts.
IMPORTANT! Use locktight on the converter bolts, and the correct sized wrench or socket (im going to guess 9/16ths or 5/8ths) because if the Converter bolts back out they will take out your starter and possibly get hung and cause major damage!
Hope this helps, if you have any questions please feel free to ask. Btw if you do sustain any damage to that trans, its mostly just going to be a front pump which can be easially replace by any local tranny shop, however look out for damage on the front input shaft for scratches or bending.
