Ok, I finally have it somewhat working. I can now read my variables, I can read what's programmed into the eeprom. The only problem is when I send values to my eeprom in my write loop it only programs the value of "50" to the memory. What am I missing?

Code:
' program for pic18f14k50
'                     u = Program EEPROM
'                    k = Dump EEPROM
'                     f = verify connection
'                     c = send last I/O values to PC
 Include "cdc_desc.bas" ' Include the HID descriptors
 Define  OSC     48
 Define  ADC_BITS 10
 Define  ADC_clock 6
 Define  ADC_sampleus 3
' initial EEPROM values (output = input)
DATA WORD 0,WORD 16,WORD 32,WORD 48,WORD 64,WORD 80,WORD 96,WORD 112,WORD 128
DATA WORD 144,WORD 160,WORD 176,WORD 192,WORD 208,WORD 224,WORD 240,WORD 256
DATA WORD 272,WORD 288,WORD 304,WORD 320,WORD 336,WORD 352,WORD 368,WORD 384
DATA WORD 400,WORD 416,WORD 432,WORD 448,WORD 464,WORD 480,WORD 496
DATA WORD 512,WORD 539,WORD 566,WORD 593,WORD 620,WORD 647,WORD 674,WORD 701,WORD 727
DATA WORD 754,WORD 781,WORD 808,WORD 835,WORD 862,WORD 889,WORD 916,WORD 943
DATA WORD 970,WORD 997,WORD 1024,WORD 1024,WORD 1024,WORD 1024,WORD 1024,WORD 1024
DATA WORD 1024,WORD 1024,WORD 1024,WORD 1024,WORD 1024,WORD 1024,WORD 1024
DATA WORD 1024
EEPROM 230, [254,0,210,0,190,0,100,0,60,0,40,0,30,0,0,0] 'temp out table word size ohm out values
'eeprom 244, [147,147,130,130,125,125,125,120,120,115,115,115,115,115,115,115] 'desired afr table
'eeprom 250, [122,0] 'displacement scalar
'eeprom 252, [ 50] 'min load for auto tune
eeprom 253, [ 64] 'tube size  scalar  tube area
eeprom 255,[ 254] 'autotune check bit
 
EWRITE var byte
EPROMDUMP var byte
BUFFER Var Byte[16]
CNT Var Byte[16]
MAFIN var word      ' 10 bit a/d input value
MAFOUT var byte[6]  ' string for usb debugging
OUTPUTVAL VAR WORD  ' output value to DAC
TEMPVAL VAR WORD    ' input temporary
TABLEHIGH VAR WORD  ' high table value
TABLELOW VAR WORD   ' low table value
TEMPVAL2 VAR WORD   ' input temporary #2
FLOW var word       ' flow value from input lookup table
inputtable con ext
MAFSCALAR var word  ' scalar for input flow value correction
FLOWINVAL var word  ' output temporary
FLOWINVAL2 var word ' output temporary #2
FLOWFINAL var word  ' flow value after mafscalar correction
ACTION var byte
CHAR var byte
inbyte var byte
X var byte
TRISC = %11000000 'make port c6,7 input make port c 012345 input
ADCON2 = %10000000

ANSELH = %00000010

 USBInit   ' Get USB going
 HIGH PORTC.2      ' Serial D-A chip select off
 
startloop:
 

 goto overdata
'0-5v input sensor transfer function in 2.9 tube adc counts to flow
asm
inputtable
 DW 0, 0, 0, 0, 0, 7, 12, 16, 20, 24, 28, 33, 39, 45, 53, 62, 72, 83, 94, 107
 DW 121, 136, 152, 169, 188, 208, 229, 252, 277, 304, 332, 363, 395, 430, 468
 DW 507, 549, 594, 641, 691, 743, 798, 855, 915, 977, 1043, 1110, 1181, 1255
 DW 1331, 1410, 1493, 1579, 1668, 1761, 1858, 1960, 2065, 2175, 2289, 2408, 2532
 DW 2659, 2791, 2925, 2925
endasm
overdata:
 usbservice
doloop:
       inbyte = 1
       USBin 3, action, inbyte, doloop2        ' Get a char from serial port
verify:
       IF action = 102 THEN   ' Verify connection
       USBout 3, action, 1, verify
       ENDIF    ' end of verify action
       IF action = 117 THEN  ' Write EEPROM
       
       X = 0
writeloop:
      USBSERVICE
      USBin 2, EWRITE, inbyte, writeloop
      
      WRITE X, EWRITE
      USBout 2, EWRITE, 1, writeloop
      X = X+1
      IF X < 10 THEN writeloop   ' this will get changed to 255 when it works.
USBSERVICE
      
      
       ENDIF ' end of Write action
valuesout:
       IF action = 99 THEN    ' Return last input and output
       USBout 3, mafout, 6, valuesout
       ENDIF ' end of IO action
       IF action = 107 THEN   ' Dump EEPROM
       X = 0
dumploop:
       
  FOR X = 1 TO 20      'this will get changed to 255 to dump the whole eeprom when it all works
    READ X, epromdump
    USBOut 3, epromdump, 1, dumploop
 pause 100
 usbservice
        NEXT
 ENDIF

     
tlabel6:
     
     
     '  ENDIF ' end of Dump action