Howdy Back Mel:
Right. The stock '69 head gasket used on all sixes was a steel shim type at .025" thick. They are no longer available. Aftermarket replacements are a composite type for better sealing, but are about .050" thick depending on brand. So the 1st .025" is to compensate for the thicker replacement head gasket.
The stock '69 250 had an advertized CR of 9:1. I don't believe it. Every 250 head and block I've been able to measure has a combustion chamber volume of 62 cc, and a deck clearance of .100" or more. In '72 the advertized CR dropped to 8:1, with no apparent change in piston, chamber volume or deck height. Clearly, 8:1 is more accurate. Milling an additional .025" will up your ratio to approximatel 8.5:1. Still within the range for using regular 85/87 octane gas. The extra CR will help with low end torque too.
I agree with you on the port divider with headers. I hand fitted mine to fit very tight. Then had it welded in as per the install instructions. I had my head flow tested before selecting the cam. While on the bench the tech used a short piece of exhaust pipe to hold to the outlet of the port as air was flowed from the chamber. Placing the pipe up to the port outlet increased flow. We tried the center siamized port both with and without the divider. The head pipe made little difference without the divider and port flow was down. With the divider in place flow was comparable with the other ports. While it is true that flow benches do not equate to HP, this was proof enough for me. I can't give a true before and after comparison because other changes were made at the same time, but I'm with you, I don't see how it can hurt, if properly installed. If it comes loose and rattles that would not be good. I also believe that anything that can help the exhaust side on these engines is good. Will you notice it in your application? Probably not, probably most noticeable with a performance cam and higher rpm applications, and then you'd need a dyno and individual cylinder temp reading to know.
Yea, I forgot about the carb bolt pattern differences. The CFM restriction is in the venturi, the throat above the butterfly. A larger throttle bore will not make up for a smaller venturi. Your combo of the YF and the Petronix are right on. You should notice much smoother engine operations.
PS- do take the time to remove the stock rocker shaft for a thorough cleaning on the inside. You will be amased at the buildup of crud and sludge. Also check both oil holes on each rocker to make sure they are fully open. We use a 1/8" drill to open the holes slightly.