Hi,
So, you're using TMR1 on the 16F628 and TMR0 on the 16F88?

If operating at 4MHz and with the prescaler set to 1:256 TMR0 will overflow at around 15Hz.
The line: IF T0Count = 512 THEN T0Count = 0 : TOGGLE LED2 doesn't work the way I think you want. The TOGGLE command will execute each time - not only when T0Count = 512. So the LED toggles at 15Hz.

I'm not sure you're actually setting up TMR0 correctly with that weird AND/OR stuff, at least it doesn't seem to match the comment in your code.
To me it looks like the end result of that operation would be OPTION_REG = %10000001 which means a prescaler of 1:4 so the LED is toggling at ~976Hz. If you want the pullups disabled, TMR0 operating as a timer with a prescaler of 1:256 then simply write OPTION_REG = %10000111

/Henrik.