Possible causes of dead cyclone IV on custom board

Well done for persisting, top marks for effort...

In answer to your questions:

1) I assume by this you mean you connected the pull-ups on TDI & TMS to 3.3V? That, on it's own, is not enough to fry your JTAG circuitry.

2) Solder bridges could cause a problem. However, frequently they simply prevent the FPGA working properly - until you remove the bridge, or they cause your power supply a problem due to excessive load.

3) Yes, you could damage it with heat - although they are pretty tolerant. I suspect the lack of accuracy in the temperature control you describe won't help.

If looking at the JTAG signals with an oscilloscope, as you mention, you're looking for something on TDO. It's perfectly acceptable for TCK to vary in frequency and (perhaps) try different ones. Do you seen any activity on TDI or TMS?

It's perfectly valid to power all the I/O at 3.3V, providing VCCA is 2.5V.

Have a look at post 49934 (http://www.alteraforum.com/forum/showthread.php?t=49934) which covers the things you need to do. Post# 7 of that summarises what you need to consider before writing off your device.

Cheers,

Alex