Q: What is the best way to simulate the PLL for
stability?  Would doing the Bode plot of the
open-loop gain equation with MathLab or equivalent graphical tool be sufficient? 

I can think of four ways to assess the PLL's
stability.

1) Measure phase margin of open-loop transfer
function at zero gain. - your suggestion.

2) Look at the amount of peaking in the
closed-loop amplitude tranfer function.
Compare results to results for known damping factors.

3) Use the damping factor equation for a 2nd-order
loop. Reasonably valid if C2 < C1/10.

4) In a transient simulation, step the reference
phase and examine the control voltage settling
behavior. You can compare settling to expected
settling for a 2nd-order loop. i.e. damped
oscillation for damping factor < 1.

I'll try to post example Matlab input files
in the next few weeks. I also have a Perl script
that calculates open and closed loop transfer
functions for a 3rd-order PLL. I'll try to post that 
as well.