To my knowledge, there's no limit!
And you can even go with a 90 day tourist visa, and on your last day fly to Korea for the night, then come back to Japan and they'll issue you another 90 day tourist visa on arrival. They say that they will catch on to it eventually though.
I admit it sucks, I'd feel bad abusing the Japanese system but sometimes you do what you've got to do, I guess..

From what I have been told, the limit is now three times in a year, and there cannot be more than 120 days in a 6 month period. So basically, you can do the Korea thing once but will have to be gone for quite a while before you can enter the country again in the same year... It is my understanding that they want you to be gone 6 months after a second entry.
There tends to be a lot of suspicion toward anyone wanting to be in Japan more than half a year as a tourist.

When it comes to transferring to a spousal visa, there really is no need to worry about the timing. As long as the visa is being processed, you receive an extension to your tourist visa. Technically, you could apply for it the last day of your tourist visa and receive an "in-processing" extension until the visa comes through... Although that would be very poor planning and they might not be very happy to accept the application (which could be a strike against it being accepted.)

I think that when we applied, we did it a couple days after getting married... Which is incredibly simple and easy to do.