[Will]

If the distributor is in a tooth or two off all that will happen is that you may not be able to rotate the distributor body far enough to get the timing set where it needs to be before the vac advance hits something.

Since you were able to see the timing marks before and had the timing adjusted, it's unlikely the distributor somehow magically jumped a tooth.

Get the wiring harness back in and leave the vac. advance unhooked and the vac port on the carb plugged until you have the engine running the way you want. Then you can start playing around with the vac advance.

The purpose of vac. advance is to help the engine run more efficiently during part-throttle cruising when AF ratios are very lean. It helps improve gas mileage and that's about it. A well tuned engine with an appropriate timing curve should run just as well in normal driving with the vac can hooked up or not.