I used a HF motorcycle jack, it really worked fine. I got pretty good at stabbing the tranny since I had ti put it in and take it out 3 times (due to my inexperience and impatience) before I finally bolted it up. Each time the tranny slid in there like...well, this is a family forum...but it went pretty easy.
The best way to seat the torque converter was to stand the tranny on it's backside (I did it onto a piece of styrofoam to protect the output shaft) so that the bell housing was sticking UP. Then rotate the torque converter until it clicked in to each of the 3 positions, the last one being a fairly profound "clunk". Then I made sure that it did not move from that spot by putting the styrofoam on the shout and taping it across the bell housing until just before I got the tranny up to the engine.
The tranny should slide up to the engine and with a little tilting and shoving it should land right on the dowels. You should not have to crank the bolts to suck it up to the engine. Mine slid on there and I was able to just finger tighten the bolts all the way up.
You are on the right track with having to lower and raise the jack "just a hair" until it lines up. Sometimes it ends up that lowering the jack actually makes the business end of the tranny go up (go figure). But it does take a bit of finesse to get it straight both sideways and lengthwise. Keep trying...and by no means should you have to use the nuts/bolts to "pull" the tranny on to the engine. If it's not just right and you end up having to crank on the bolts, things will end up binding and breaking things.