You may even be pushed for time. KL immigration is pretty slow with everybody being finger printed inc children. The train go's around every 15 minutes and takes around 10-15 minutes between terminals
I've never yet been able to stay airside while on a transit involving 2 airlines. I've always had to clear security and immigration then check in to the airline desk and go back through. Different if your with the same airline. It also makes a difference on what time your return next flight is. They mostly dont want you hanging around airside for hours.
Unless your Japanese or have the residents card, I don't believe any visa is possible in Japan
For non-Japanese applicant, a copy of residence card or certificate of alien registration which is valid at least 3 months or more. For those who are currently applying for renewal of residence card, please submit a copy of acceptance of renewal issued by Immigration Bureau of Japan. The applicant is also required to present the original documents of identification upon visa application.