Well.... I'm trying to help...
It's so hard to do this via emails - or in this case posts... so I'm just thinking and posting as I can come up with somewhere else to look.
RE: Ported / unported manifold vac
Timing is typically "set" (the initial timing or "static" timing as it's sometimes called) with the vaccum line to the distributor disconnected and plugged (so it doesn't cause a vacuum leak). So let's say that is set at 10*
If you then reconnect the line to ported (manifold) vacuum... you are going to be adding vacuum thus also adding "advance" and changing the initial timing.
If the car runs better with MORE initial timing --- then what should be done is to set the distributor up (stop bushings etc) so that it is timed at the proper initial timing (let's say 14*)... without the aid of the vacuum advance. Not sure what distributor you're running but a quick check on the internet to the manufacturers website should give you info on what (if anything) you have to do to set the proper stop bushing and adjust your timing CURVE. THESE settings are CRITICAL to the performance and overall operation of the motor.
You want to have the initial advance be set... at whatever the motor WANTS... there is no 'book' on this - so it's a "where it likes it" kind of setting... BUT --- then whatever that number is -- needs to be SUBTRACTED from the TOTAL TIMING number (let's say 36*).... so if you set initial at 14* and want a total of 36* -- you need to LIMIT the mechanical advance to 22*. You do this via stop bushings in an MSD.
The vacuum advance would then be connected to the PORTED vacuum (NO vacuum at idle) and would only pull vacuum when driving... and even that needs to be checked to see how much advance it's adding while cruising. That's another discussion.
There should be springs etc -- or some way to adjust the timing CURVE on your distributor. The rate of mechanical advance is important -- too much causes problems and too little will rob you of power and give you different problems. Sometimes this requires a good educated guess... and seat of the pants testing --- or a dyno is the best place -- because timing is everything.
RE: MSD BOX --- Yes by all means I'd add this. They work great and certainly would be worth the small cost.