>>How to repair an Excalibur Development Board?

Did you do anything hardware related external to the FPGA or did this just happen one day when you went to program it (i.e. was it running with this design fine the all of the sudden one day you get thermal issues?).

When an FPGA gets too hot some of the internals will not operate properly (perhaps that's why your timer isn't working).

I've seen someone make a design that got very hot before but he did it using methods I'm surprised quartus let him get away with. I guess check your I/O to making sure your not driving pins to hardwired outputs (Vcc to Gnd and visa versa). I'm pretty sure that device had current limiting too but if you drive lets say 40mA on a lot of I/O then it'll get very warm. In the quartus project set all unused I/O to tri-state just to be sure (up in the device options area).

Another quick test you can try is to create a new design and route two push button switches through an AND gate and out to a led. Let it stay up for a while to be sure that not too much heat is created (because I'm thinking if the heat issue is internal due to damage, then you're going to have a short that creates heat no matter what design is in there). Also when you check for the heat either use some type of thermometer that can get at the heat sync temp properly, or if you are going to touch the FPGA make sure you are grounded to the same common ground so that you don't discharge static electricity into the FPGA.

If you have further questions for me, post them and cut and paste it in an email to me as well because I'm not around much lately so I would take forever to get back to you otherwise (email is in my profile)

Cheers and goodluck (thermal issues are one of the nastiest things to fix in the digital world)