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. )
