Checking Arduino Mega 2560, may have zapped it!!!!

I was working on a shield for the Mega and when testing the shield I had a short that zapped the mega. I have an Uno and was able to use it to check the bootloader's integrity and found errors. Also used the UNO to load the bootloader again as per the instruction found at: http://www.gammon.com.au/forum/?id=11635

Checked bootloader for errors again and none are found. However, my programs (sketches) don't work. I used the instructions found at: Bootloader for Arduino Mega2560 to check the mega's bootloader's monitor and everything seems to check out except the vectors they are all blank...

Can anyone double check the settings and help/point me to the fix if there is a problem? I think the vectors are missing... Much appreciated...

Here are the results from the monitor:

Blink LED works
Blink port works
"0" just returns 0 Zero addr

Bootloader>? CPU stats
Arduino explorer stk500V2 by MLS
Compiled on = May  8 2012
CPU Type    = ATmega2560
__AVR_ARCH__= 6
GCC Version = 4.3.3
AVR LibC Ver= 1.6.7
CPU ID      = 1E9801
Low fuse    = FF
High fuse   = D8
Ext fuse    = FD
Lock fuse   = EF
Bootloader>E Dump EEPROM
0000 - 41 72 64 75 69 6E 6F 20 65 78 70 6C 6F 72 65 72 Arduino explorer
0010 - 20 73 74 6B 35 30 30 56 32 20 62 79 20 4D 4C 53  stk500V2 by MLS
0020 - 00 42 6F 6F 74 6C 6F 61 64 65 72 3E 00 48 75 68 .Bootloader>.Huh
0030 - 3F 00 43 6F 6D 70 69 6C 65 64 20 6F 6E 20 3D 20 ?.Compiled on = 
0040 - 00 43 50 55 20 54 79 70 65 20 20 20 20 3D 20 00 .CPU Type    = .
0050 - 5F 5F 41 56 52 5F 41 52 43 48 5F 5F 3D 20 00 41 __AVR_ARCH__= .A
0060 - 56 52 20 4C 69 62 43 20 56 65 72 3D 20 00 47 43 VR LibC Ver= .GC
0070 - 43 20 56 65 72 73 69 6F 6E 20 3D 20 00 43 50 55 C Version = .CPU
0080 - 20 49 44 20 20 20 20 20 20 3D 20 00 4C 6F 77 20  ID      = .Low 
0090 - 66 75 73 65 20 20 20 20 3D 20 00 48 69 67 68 20 fuse    = .High 
00A0 - 66 75 73 65 20 20 20 3D 20 00 45 78 74 20 66 75 fuse   = .Ext fu
00B0 - 73 65 20 20 20 20 3D 20 00 4C 6F 63 6B 20 66 75 se    = .Lock fu
00C0 - 73 65 20 20 20 3D 20 00 4D 61 79 20 20 38 20 32 se   = .May  8 2
00D0 - 30 31 32 00 31 2E 36 2E 37 00 34 2E 33 2E 33 00 012.1.6.7.4.3.3.
00E0 - 56 23 20 20 20 41 44 44 52 20 20 20 6F 70 20 63 V#   ADDR   op c
00F0 - 6F 64 65 20 20 20 20 20 69 6E 73 74 72 75 63 74 ode     instruct
Bootloader>F Dump FLASH
0000 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0010 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0020 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0030 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0040 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0050 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0060 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0070 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0080 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
0090 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
00A0 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
00B0 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
00C0 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
00D0 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
00E0 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
00F0 - FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF ................
Bootloader>V show interrupt Vectors
ATmega2560
V#   ADDR   op code     instruction addr   Interrupt
01 - 0000 = FF FF FF FF no vector
02 - 0002 = FF FF FF FF no vector
03 - 0004 = FF FF FF FF no vector
04 - 0006 = FF FF FF FF no vector
05 - 0008 = FF FF FF FF no vector
06 - 000A = FF FF FF FF no vector
07 - 000C = FF FF FF FF no vector
08 - 000E = FF FF FF FF no vector
09 - 0010 = FF FF FF FF no vector
10 - 0012 = FF FF FF FF no vector
11 - 0014 = FF FF FF FF no vector
12 - 0016 = FF FF FF FF no vector
13 - 0018 = FF FF FF FF no vector
14 - 001A = FF FF FF FF no vector
15 - 001C = FF FF FF FF no vector
16 - 001E = FF FF FF FF no vector
17 - 0020 = FF FF FF FF no vector
18 - 0022 = FF FF FF FF no vector
19 - 0024 = FF FF FF FF no vector
20 - 0026 = FF FF FF FF no vector
21 - 0028 = FF FF FF FF no vector
22 - 002A = FF FF FF FF no vector
23 - 002C = FF FF FF FF no vector
24 - 002E = FF FF FF FF no vector
25 - 0030 = FF FF FF FF no vector
26 - 0032 = FF FF FF FF no vector
27 - 0034 = FF FF FF FF no vector
28 - 0036 = FF FF FF FF no vector
29 - 0038 = FF FF FF FF no vector
30 - 003A = FF FF FF FF no vector
31 - 003C = FF FF FF FF no vector
32 - 003E = FF FF FF FF no vector
33 - 0040 = FF FF FF FF no vector
34 - 0042 = FF FF FF FF no vector
35 - 0044 = FF FF FF FF no vector
36 - 0046 = FF FF FF FF no vector
37 - 0048 = FF FF FF FF no vector
38 - 004A = FF FF FF FF no vector
39 - 004C = FF FF FF FF no vector
40 - 004E = FF FF FF FF no vector
41 - 0050 = FF FF FF FF no vector
42 - 0052 = FF FF FF FF no vector
43 - 0054 = FF FF FF FF no vector
44 - 0056 = FF FF FF FF no vector
45 - 0058 = FF FF FF FF no vector
46 - 005A = FF FF FF FF no vector
47 - 005C = FF FF FF FF no vector
48 - 005E = FF FF FF FF no vector
49 - 0060 = FF FF FF FF no vector
50 - 0062 = FF FF FF FF no vector
51 - 0064 = FF FF FF FF no vector
52 - 0066 = FF FF FF FF no vector
53 - 0068 = FF FF FF FF no vector
54 - 006A = FF FF FF FF no vector
55 - 006C = FF FF FF FF no vector
56 - 006E = FF FF FF FF no vector
57 - 0070 = FF FF FF FF no vector