Kaushal,
First tip is that if you are looking for more detail on Freescale's 1588 PTP engine, you will find more about the IEEE 1588 engine in the MPC8360E reference manual than you will in the MPC8313E manual.
The only "timing diagram" I have ever seen in regards to the 1588 PTP engine in any Freescale 83xx manual is in section 31.11.2 of the MPC8360E manual which shows the relation between the Pulse Output and the output reference clock.
The Output reference clock is driven as a simple divisor to whatever clock source is input into the 1588 engine. It is then divided by whatever number you put into the prescale register. So if the 1588 engine is driven with a 133 Mhz system clock, and the divisor is set to one, then you'll get a 133 Mhz clock synchronized to the system clock. If you program the register to 2, then you get a 66 Mhz clock still synchronized to that clock, but at half the rate.
Here is an excerpt on the timer prescale register from section 31.9.6.
Output clock division/prescale factor. Output clock is generated by dividing the timer input clock by this number. Setting the prescaler value to "1" will generate an output clock in the same frequency as the system timer register.
So my understanding of the engine is that as it is doing an integer divide on whatever clock you put in and that the selectable 1588 input clock drives the engine, so you should get as good a clock as you put into the chip to drive the 1588 engine.
Here is a link to the 8360E reference manual if you don't already have a copy:
Hope this helps,
Alan
P.S. I am a SW engineer and not a HW engineer so if you need more data than this, you may have to contact your Freescale rep for more detailed info (or perhaps someone with direct HW experience with this can post a reply).