Unfortunately, when you return to the UK in three or four years time, your wife's ILR will have lapsed. As others have mentioned, this happens when she hasn't been living in the UK for two years.
When you do wish to return, you will be applying for a new spouse visa. You won't get any "credit" for time already in the UK. Moreover, you will be subject to the new rules that just came into force on the 9th of July.
To return, your wife will apply for her first spouse visa overseas at a cost of more than a thousand pounds. This will be valid for 30 months. At the end of those thirty months, she will have to extend that spousal visa for another 30 months. Again at a cost of more than a thousand pounds, and the fees go up all the time.
After those 60 months are up (or 5 years), then she can apply for ILR again, also at a cost of more than a thousand pounds. Note that the qualifying period for the spousal ILR route has increased from two years to five.
I understand that Japan doesn't easily tolerate dual citizenship. If she becomes British, she will likely have to give up her Japanese nationality. But I guess this is something that the OP has to balance against the hassle and cost of starting the settlement process all over again.
See this:
http://www.ukba.homeoffice.gov.uk/visas ... spouse-cp/
And particularly this:
http://www.ukba.homeoffice.gov.uk/sitec ... family-mig
