It is super straight forward. I just helped my buddy with this. His website has some way cool write ups
mestiso.net he has donetons of stuff to his car and loves to do write ups.
Like others have said you can keep your stock auto ecu, you have to jump the park lock under the relay box in the engine compartment. You will need more than just the tranny...ie flywheel, clutch, flywheel bolts, belhousing bolts, manusl drive shaft, manual tranny mount, clutch master and slave, clutch lines hard and soft, upper and lower, shift boots, gear oil, a nice level place to do it, and a little patience.
While doing it it is a great time to replace your rear main seal. Buy a new clutch, soft line, master, and slave cylinder. It is a great time to replace your steering box bushings since you are right there.
It is not that bad, but a word of advice get all you stuff first before you tear your car apart. You don't want to have it all apart and find out you do not have the right flywheel bolts, or your slave cylinder is on back-order.
Feel free to ask any questions of me or mestiso about the swap.