1. The Narita airport website has a good guide to arrival procedures. It looks like a lot, but in practice the quarantine steps are only for certain circumstances. You would usually walk straight past the people at step 1 unless you look like a hospital case. The whole thing is very efficient. I've got through in as little as 15 minutes.
Information on departure and arrival procedures | NARITA INTERNATIONAL AIRPORT OFFICIAL WEBSITE
2. A couple of hours beforehand is fine.
3.If you've done any tax-free shopping while in Japan, there will be some forms stapled inside your passport. You're supposed to have these collected at the airport, but sometimes this doesn't happen. Just remove them yourself once you're through to the departure area.
4. Bringing some cash is useful. Otherwise use ATMs - 7-11 and Japan Post ATMs are reliable with foreign cards.