I am a Navy Veteran and spouse of a Japanese National who has lived in Japan for over 20 years and have a permanent residency visa. 

I have just been offered a base job and was wondering if there was anyone out there who has had this experience lately and can give me the low down.

The questions are as follows:

I have paid Japanese income tax for over 20 years and they usually take last year's salary to decide your tax for the following year, do they do this for us once we are on a SOFA Visa or do they just clear it as if you didn't live here?

I own a house here in Japan and we must pay house/property tax do I still have to do this after taking SOFA sponsorship.

Is there anywhere or anyone we can talk to about all of these issues?  Time is short as they will hopefully be making the official offer in the near future.

HELP NEEDED!

I would call the legal office of the base where you are getting a job. You could put the property in your wife's name and that would not be a problem I think. I think might lose you Japan pension. I got out but I was a spouse visa for like a second. I hope people will chime in. good luck. You are local hire right? no housing allowance or anything?

I lived in Japan on work, SOFA, and spouse visas at different times..

You won't be liable for paying Japanese income taxes once you get SOFA. For all intents an purposes you will no longer be living in Japan when it comes to income tax.

You will, however, still have to pay property tax.

The only gray area you will run into is paying into the national health insurance system. To continue to have access, you will have to pay something. The Japanese government has no way of tracking your income on base if you have SOFA so how much you declare will really be on the honor system. You could probably get away with telling them you are retired and not have to pay much at all. I never declared any income with them at all.

You have to pay the property tax. The GOJ will probably demand you surrender your alien ID card once you obtain SOFA, if you do not turn it in then you are liable for JN income tax even though you are SOFA. The GOJ may not bother you for 3 or 4 years but if you don't turn in the card they will eventaully demand back taxes. You can keep the JN health insurance as long as you pay the premium.
The only way around this is if you are retired, in that case you can claim that your JN wife is your sponsor and you do not work, even though you are actaully SOFA sponsored. To do this you have to show the GOJ your retired ID, passport and LES to show that you have income. You can straddle the fence by going this route but if the GOJ finds out that you were actaully SOFA it won't pleasant for you (all it takes is an off base traffic accident for them to find out, or a SOFA stamp in your passport).
Go to legal, don't try to game the system,a friend in Yokohama tried to scam the sytem and was nailed for $15,000 US in JN taxes, as you prbably know the GOJ wanted the money in a lump sum as they don't play the easy payment plan game.