Do you know how to get the Secondery error codes for rrod? Wait till RROD then hold sync, then press eject, the ROL will flash a code, on the 1st press it will flash 1st number, then still holding sync press eject again, this will give 2nd number, repeat this 4 times, for the code, the 5th press should return it to your original RROD, unless there is more than one problem where it may flash out another 4 digit code.
4LEDs = 0
1LED = 1
2LEDs = 2
3LEDs = 3
Once you have the code look here for more info http://forums.xbox-scene.com/index.php?showtopic=484726
I would imagine it will be 0022 or something CPU related.
Looking at your pictures it looks like you have also torn off the pad at point CPU_PLL_BYPASS, the one on bottom side of CPU, look back at the page I posted before on how to repair this point. Your STBY_CLK point looks like it should be ok, its ugly but should be ok, just remove that little bit of trace wire thas hanging off from where the blob of glue is.
You can leave the nand reader attached this wont interfere with anything.