Hi Mustang66,
Sorry to hear about your frustration. Sounds like you are dealing with several issues. Need to break this down to one at a time. Let's start with the ignition since that seems to be the number one headache.
First, the Pertronix II and Flamethrower 2 are a very good upgrade. However, as you know the the electrical source is key. So is being sure you have the correct unit for the dizzy, thermactor or not. Call Pertronics and verify with them that you have the correct part number. The '67 dizzy could be either one (91266 or 91261 - "D" drive or "KEY drive and I don't remember which is which).
Did you remove the Ballast Resistor?? Have you checked the voltage at the + (red) side of the coil. The PII with F2 are designed to run w/o the resistor, i.e., 12 volt coil and dizzy. Remove the resistor, be sure you have 12 volts at the coil, and hook the red dizzy line to the + side of the coil. Be sure all connections are clean / tight. Be sure the PII is gapped correctly (.030). Replace your cap and rotor as worn parts don't stand up to 45000 volts very well. New / good plugs should be gapped at 45 for starters.
Timing. The 200 I6 likes a lot of initial advance. 20* with a stock cam is not shocking. The problem is that with 20* initial you will very likely have an overadvanced condition under accelleration. The all-in advance should not exceed 34* - 38* at 2400 - 2600 rpm. If you are sure you have the dual advance dizzy (single vac), try this. Disconnect the vac advance, i.e., plug the vac at the dizzy and the carb. Set the timing at 20* at 600 rpm (in gear if you have an automatic). The slower the better (500 - 600) so as to insure that the mechanical advance has not kicked in. After set increase the idle to whatever seem best setting (mine likes 700 in gear). Do not hook up the vac sustem. Drive the car. If you get ping under load (WOT accelleration) back off the initial advance until it goes away (set & drive, set & drive, etc - my car likes 16*). It is entirely possible that the vac system is overadvancing the car. See this sight
www.bob2000.com/dist.htm.
I am a strong supporter of the mechanical advance only system primarily because it is the only way to know exectly what your timing advance curve and rate are going to be under all driving conditions. The vac system introduces to many variables. In your case, however, I am concerned that the vac system on the 1100 carb may not be compatible with the dual advance dizzy. The best way to check is to bypass it. I suspect you will see the benefits as soon as you try this. The only down side is that we don't know which advance weight limit you currently have (see
www.bob2000). If the dizzy you purchased has a 15* weight, you will have 30* at 2500 rpm B4 initial or vac advance is introduced. If you find that you have to reduce you initial to something on the order of 5* - 6* to eliminate ping, you have the wrong weight for a mechanical advance only system (
www.bob2000). Also, at 5* initial your car will idle like C..p. If this is the case, however, this is the exact reason for the vac system. If hooked to a ported source the vac advance should add approx 10* at idle. Then, in theory, as the throttle is opened (WOT accelleration) the vac deminishes and the car gets only the initial + the mechanical (5* + 30* = 35*). The problem is that you can't be sure what the vac is actually doing at any point in the rpm / load cycle. But that is how it is intended to work. So, if you get down to 5*, you should see idle improve when you hook up the vac. However, the 1100 vac system was intended to run with a dual vac dizzy. It, therefore, has a valve in the vac port that could interfer with the advance signal your dizzy needs, + or -. The fix is to run the car with mechanical advance only so long as you stay with the 1100. Actually, I like the mechanical for any carb application. To convert, you simply need to put the 10* weight limit in the dizzy and set the initial at the highest possible "no ping" level.
If ignition and timing adjustments alone don't correct your issues you will need to consider the carb, value adjustment and timing (rockers and chain), etc. But with a newly rebuilt motor I doubt etc is an issue. At any rate, take these systems on one at a time.
Hope this helps. I had a very similar problem with my '66 200. The process was expensive (many mistakes) amd frustrating, but when it all comes togather it feels GOOD.
Enjoy the trip - Steve