You need to do a wiggle test. The clutch cables on that particular car is a real pain, and for someone who hasn't done it before, it's really easy to screw up wiring. My friend is a Hyundai Master Tech and hates working on them because of routing and space. It's sounding like a short somewhere, but you need to determine where.
Get yourself a new fuse, put it in. Start the car and find any and all harnesses you can near the vicinity of the fusebox and under the dash. It comes in under the brake master cylinder, and travels all the way to the ECU on the right passenger side. Gently wiggle on the harness until you can blow the fuse or get the ECU to stop working. There are much more expensive ways to do this professionally, but the tools are pretty expensive.
Here's the link if you're interested.
It's never failed me and cheaper now. I paid $500 for mine. That's a steal for something like that.