Hi,
Too many questions at the same time for me.... I'll start with the first one:
-In a 16F628A, I receive a pulse into a timer, in counter mode, let's say timer1.
Question:
-Is there any kind of interrupt flag or trick that tells me when it matches a specified count? (example: when TMR1=231)
There's at least two ways of doing this as I see it. Either you preset the TMR register with 65535-231 (for a 16bit timer) and when the timer/counter overflows you'll get your interrupt. OR you can use the CCP-module in compare mode, it's designed for doing exactly that. When TMR1 matches the CCPR1 register you'll get an interrupt.

/Henrik.