[MENTION=190086]brisamh[/MENTION]
There exists a M/T ECU for your 2000 (if you have a 5VZ) that’s plug and play. If you can tell me your A/T ECU part number (you don’t even have to remove it to see the part number: Remove the glove box, remove the three 10mm hex bolts holding the black trim behind the glove box, unhook the trim from the sides and from the wire loom, and take your phone and stick it up above and in front of the ECU and take a picture with the flash on...should take 5 minutes to take apart, take a picture, and put back together) I can tell you what M/T ECU part number is a perfect match.
As for the anti-theft stuff, do you have a red blinking security light either on the left side of your steering wheel or next to the back window up/down switch in the center dash? If you don’t, you don’t have to worry about anything else. If you do, then on the new ECU you will have to get the IC900 chip reflashed with an EEPROM chip reader and re-program all your keys, or copy over the values from your A/T ECU chip over the the M/T ECU chip. Any certified locksmith should be able to do that for ~$200.