i think the first thing you should do is invest in a soldering iron and some waterproof shrink tube. those wire crimp things are not a positive conection and will only get worse over time as moisture finds its way into the wires. wire connecters like that have no place in automotive applications as far as im concerned. 
if your real lucky maybe that will fix the issue but my guess is you may have damaged the computer.
yeah. I actually had my soldering iron on hand, but no plug for a hundred yards so the crimps were supposed to be a temporary measure...
My other thought would are you 100% you didnt hit any other wires?
I did the same thing in my cummins tryig to mount my fire extinguisher bracket. I was lucky and basically just cut the wire insulation and grounded the wire or something. Taped the insulation up, and replaced my fuse and was good to go. 
What is the part number on your ecu? I have an extra one from a 99 3.4l automatic you could borrow to see if it is fried? (I dont know anything about tacomas, i dont even know if you have a 3.4. )
i couldn't see any other wires that were damaged. It's a 2004 double cab with the 3.4 automatic. I'm in central Utah.... I don't know the part number of the computer
My plan of attack will probably be unplug it for a while, and solder and heat shrink while it's unplugged. If that doesn't help then it might be time to haul it to a shop...
