It depends on what prefecture you'll be in as to how picky they are about things.
Re the scooter test: Some prefectures do offer it in English. Others don't. But you have to take the test in the prefecture that's listed as your address on your gaijin card. So you may be SOL. However, if you have a regular Japanese license for cars you can also drive scooters up to a certain size (I forget exactly what that is off the top of my head).
I'm assuming you'll do the kirikae process for getting a normal license. I went through it last year and had my first interview at the end of February... and after three interviews and one try at the driving test I finally got my license in June (well after my IDP had expired... ugh!)
The first step is an interview about how you got your license, your driving school (if you went to one), etc. etc. They'll also go through your passport and ask you where you've been and for how long (this is to determine if you've held your license long enough to do the conversion). I think my initial interview lasted about 2 hours. Some prefectures might be able to do the interview in English, but mine didn't. I did most of the talking, but took a Japanese friend along, mostly to put the interviewing officer at ease.
Once you get through the interview stage its onto the written test and the practical test. Written test is super easy... 10 true or false questions... mostly common sense stuff. And it's available in English.
The practical exam is a pain.... and like Tzadeck said, it has nothing to do with driving in the "real world", but how well you can execute things on a closed course. And they're really picky about that execution. Things vary from prefecture to prefecture.... but in Yamanashi there are three different courses. You're expected to memorize all three. Before the test, they ask one of the examinees to draw the course that will be used that day. The examiner just sits in the car and marks your score... they don't give any instructions to you about the course.
I managed to pass on my first try, but I paid 6500 yen for an hour of lessons on the course beforehand. The instructor took me through all three of the courses and showed me all the mirror checks, when/how they want you to switch lanes, where to align my car while turning, and the certain points where you're supposed to accelerate to a certain speed. Most people I know have had to take the test 2 or 3 times (if not more).
The reason it took me so long to get my license is because I had to go in for three separate interviews... each with different documentation from the Department of Transportation in my home state. They only give driving tests to 10% of license applicants where I'm from... so if you've had driver's ed and your birthday isn't one of the days that's been drawn to drive, you don't have to take the driving test when you first get your license.
The officer that did my interview was absolutely taken aback by this during my interview. You would've thought that I'd told him I was from Mars or something.... haha. I've had other friends have trouble with having to get immigration records and things from their home countries to go through the process. They even made a huge deal over one girls' license because it had her middle initial listed on it instead of her full middle name.
So moral of the story: they're really anal about the process, and be prepared for a really bureaucratic process (one of many you'll have here

) But worth the trouble if you live in (or travel to) an area where the public transportation leaves much to be desired.
I found this link rather helpful when I was getting ready to go through the process:
http://www.supermelf.com/japan/ajetdrivi.../index.htm
And talk to other people who have taken the test in your prefecture, as they'll be the best source for finding out how particular your testing center is.
Edited: 2009-10-28, 4:36 am