This should be simple?

[skimask]

You're adding in the overflow in OPLUS, but you aren't dropping the yvaltot value, so the next time around, it still sees the same 'almost overflowing' yvaltot, and still increments the overflow.
If I was you...and this is just one way of doing things...make yvaltot hold a value from 0-9999, then another word variable, say yvaltot_high hold the next 4 digits to the left of that...
Yes, I'm going to colonize your program, just for me
Changes in bold...

@ DEVICE pic16F689, intrc_osc_noclkout, wdt_off, mclr_off, protect_off
CM1CON0 = 0 : CM2CON0 = 0 : ADCON0 = 0 : ANSEL = 0 : ANSELH = 0 : OSCCON = $61
TRISA = %101100 : TRISB = %0000 : TRISC = 0 : OPTION_REG = $c0
Define LCD_DREG PORTC 'Set LCD data port
DEFINE LCD_DBIT 0 'Set LCD starting data bit
DEFINE LCD_RSREG PORTC 'Set LCD register select port
DEFINE LCD_RSBIT 4 'Set LCD register select bit
DEFINE LCD_EREG PORTC 'Set LCD enable port
DEFINE LCD_EBIT 5 'Set LCD enable bit
DEFINE LCD_BITS 4 'Set LCD bus size
DEFINE LCD_LINES 2 'Set LCD number of lines
DEFINE LCD_COMMANDUS 1500 'Set command delay time in us
DEFINE LCD_DATAUS 200 'Set data delay time in us
NCS VAR PORTB.5 : SPEAKER VAR PORTA.4 : MOSI VAR PORTA.0 : MISO VAR PORTA.3
DATAIN VAR BYTE : MOTBYTE var BYTE : MOTBIT var BIT : MOTBIT = MOTBYTE.BIT7
YVAL VAR BYTE : XVAL VAR BYTE : YVALTOT VAR WORD : YVALTOTHI VAR WORD
MOTBIT = 0 : LOW PORTC.6 : LOW PORTC.7 : DATAIN = 0 : PAUSE 1000 : NCS = 0
NCS = 1 : NCS = 0 : SHIFTOUT MOSI,PORTA.1,5,[$3a\8] 'Reset sensor
PAUSE 10 : SHIFTOUT MOSI,PORTA.1,5,[$5a\8] : ncs = 1 : yval = 0 : yvaltot = 0
yvaltothi = 0 : PORTB.7 = 0
Main:
ncs = 0 : shiftout mosi,PORTA.1,5,[$02\8] : PAUSE 10
SHiftin miso,PORTA.1,6,[MOTBYTE\8]  : Pause 10 : ncs = 1
If MOTByTE = $e0 then YCOUNT
LCDOUT $fe,1,dec4 yvaltothi, dec4 yvaltot
goto Main
YCOUNT:
ncs = 0 : SHIFTOUT MOSI,PORTA.1,5,[$03\8] 'input values
SHIFTIN MISO,PORTA.1,6,[YVAL\8] : SHIFTOUT MOSI,PORTA.1,5,[$04\8]
SHIFTIN MISO,PORTA.1,6,[XVAL\8] : ncs = 1
yvaltot = yvaltot + yval 'count Y values
if yvaltot > 10000 then OPLUS 'keep track of y overflows
goto Main

OPLUS:
yvaltot = yvaltot - 10000 : yvaltothi = yvaltothi + 1
goto main

END