Hmm… sounds like the ATMega16U-mu serial<->TTL chip is hung… (holding pins PD4 (RX-LED) PD5 (TX LED) (I imagine PD2 & 3 (RX-Data, TX-Data) as well, and PD7 (DTR, which applies the brief start-up reset to the 328) all high.)
Let’s see… You said You have a replacement (yes, it’s good the price is still low enough to spring for a replacement! When my MEGA2560 crashed, I found a local store that carrie the XDRduino 2560 (MEGA2560 R3 clone) for only $40 (but I’ve seen them for much less on EBay)), so that’s good… If you’re feeling adventurous, and want to see if you can revive the old one (Never hurts to keep a handy back-up!) I’ve found a few links on how to go about the 16U reset process (loading the 16U’s bootloader firmware back into the chip)… And the fun thing is, You can use the new UNO as the ISP loader!
One link, Off-site from here gives a good idea on how to go about it, including links to software for the process. You can also turn the newer UNO into a ISP programmer, (Using pins D10-D13), to the ICSP1 pins in the upper-left corner (just right of the USB socket) on the older device. Virtuabotix is under construction It also gives a link for the 16U firmware.
There’s also a discussion here on the Arduino.cc site, I ran across, also covering the process. http://forum.arduino.cc/index.php?topic=141407.0
(wiring them together, Use the shematic for the Uno R3 at http://arduino.cc/en/uploads/Main/Arduino_Uno_Rev3-schematic.pdf , to wire the pins 13 to 10, to the 6-pin ICSP1 header , D12 to MISO2, D11 to MOSI2, 13 to SCK2, and D10 to Reset2, simply jump +5 to +5, and GND to GND on both boards.) (there is also some note, of needing a 10uF capacitor across the reset on the dead UNO, but that is only for bootloading the 328 (Main MCU), so that can be ignored.)
I used a Duemilinova clone as my ISP loader on the 2560. Just took adding a set of male-female jumper wires, and following the wiring diagram in the Files->Examples->ArduinoISP sketch. (which you would upload to the new UNO), and added the Error (D8) Heartbeat (D9) and Prgm (D7) indicators, using a Protoboard plugged into the Duemilinova.
Hope some of this helps! It took me a few tries to get the 2560 functioning again, and I still got an odd error from the bootloader, even though the 2560 runs fine! Either It was seeing older 2560, and not the R3 version, or I might’ve popped one of the wrong fuses in the 2560. (haven’t gone that far yet.)