If you want to learn about PLL's, you're in exactly the right spot.
I probably shouldn't be tossing out advice here, so take anything I say as if it's from a self-mistaught amateur . . . because it is. So here are a few comments. Maybe something might be useful for you:
I started experimenting with a square wave OCXO. I ran that through a 74HCT14 Schmitt trigger and through a pair of 74HCT390 counter/dividers. My Jupiter-T has a 10 kHz output, so I needed a divide-by-1000.
I got my first PLL working using a simple XOR gate as the phase comparator. Getting lock was pretty easy, but there was a fixed delay between the rising edges of the clock and the ref. I think the best stable lock I could achieve had about a 7° phase difference.
So . . . I decided a charge pump was the way to go. Since I'm not smart enough (yet) to work out my own charge pump, I added a 74HCT7046. I'm only using the phase detectors in it -- not the VCO. After figuring out enough to make a decent loop filter, I now get consistent and reliable lockup with almost no discernable phase difference. There is some, but I think it's less than 0.5°. The PD blip on the oscilloscope looks to be about 0.1 uS wide, but I think the time measurement on my scope is a bit out of calibration.
Also, when I switched to the Morion MV89A, I needed to convert the sine wave into a square wave for the counters. I'm not sure what the *best* method is, but I tried different approaches including some in the "LPRO User's Guide & Integration Guidelines" PDF (
http://www.ham-radio.com/sbms/LPRO-101.pdf). Eventually, I settled on the Linear LTC6957 Low Phase Noise, Dual Output Buffer/Driver/Logic Converter (
http://www.linear.com/product/LTC6957-1) using their example circuit at the end of the datasheet (the one with the Coilcraft 16:1 transformer). I did have to add a simple LC impedance matching circuit, but it works great. Of course, since it's on protoboard, it's not the best environment for clean signals.
So that's about where I am. My plan is to buffer the OCXO through a common emitter amplifier (
http://www.ko4bb.com/~bruce/OCXOBufferAmplifiers.html), run it through a 0° splitter, send one copy to the PLL via the LTC6957 and the other to a signal distribution board. I'm tinkering with the digital side now; with ADC measurements of the phase detectors and getting control of the GPS from the MCU (Teensy 3.1).
I'm also considering ways to handle holdover for when the GPS loses lock. One thought is to use an analog switch to cut the control line back to the OCXO and let it free float, but that doesn't seem smart. The other is to constantly gather PLL feedback voltage statistics while there is lock, then switch to the ADC to hold it at the latest average.
Do try the simple XOR phase detector though. It's educational at the very least.