I would recommend budgeting 80,000 yen for the whole process, including the inkan. Bear in mind that you have to register for corporate tax within a month of incorporation, and I won't be posting any how-to on that one; it's a form-filling nightmare that only an accountant with a strong stomach should have to deal with. Also, although I've tried to make things as simple as possible you will still need some strong Japanese language ability on hand and a fair amount of spare time, so if you have more money than time then you might want to fob the whole thing off on a lawyer. Finally, there are many reporting and compliance requirements that come with incorporation, so you'll still need to do your homework.
If you have any questions, feel free to ask. If anything's unclear, let me know and I'll make some edits.
A useful article:
http://www.japaninc.com/mgz_autumn_2006_incorporate
Another guide, with some details not included here: http://www.juridique.jp/incorporation_bis.html
The templates (MS Word 2003 format)
The process
1.      Get an office to use as your registered company address. A regular office, an incubator, a virtual office, or even your home will do. 
2.      Create your articles of incorporation document.
3.      Go to the Legal Affairs Bureau of the ward your company office will be located in.
1.      Get a company inkan registration form and an OCR application form (actually grab a couple of OCR forms, as they’re a bit fiddly to print onto properly).
2.      Also have them look through your articles of incorporation to check they are okay.
4.      Buy a company inkan, plus a personal inkan for each director who doesn’t already have one.
5.      Each director must register their personal inkan at their local ward office, and get a personal inkan registration certificate.
6.      Complete the company inkan registration form.
7.      Choose one of the directors’ personal bank accounts that will hold startup capital, or open a new account.
8.      Transfer startup capital to the personal bank account.
9.      Produce evidence that startup capital has been deposited.
10.    Make declaration of capital deposit document.
11.    Make LLC application document.
12.    Make acceptance of responsibility as company representative document.
13.    Make decision on incorporation details document.
14.    Print out all documents.
15.    Ensure that personal and company inkan stamps are on all documents and forms where required (these are marked印and代表印respectively in the sample documents provided).
16.    Take everything to the Legal Affairs Bureau.
1.      Go to the consultation counter to have them check that the documents are okay. They will add a number of inkan stamps and staple everything together.
2.      Buy a 60,000 yen revenue stamp and stick it on the LLC application form.
3.      Submit everything to them.
4.      Pick up a company inkan registration card application form, an inkan registration certificate application form, and an incorporation certificate application form.
5.      They will give you a date to come back once the application has been processed.
17.    Return to the Legal Affairs Bureau on the set date.
1.      Submit the completed company inkan registration card application form, inkan registration certificate application form, and incorporation certificate application form, and receive your inkan registration card, inkan registration certificates, and incorporation certificates.
2.      While you’re there, you should head for the tax department and collect the mountains of forms required to register for corporate tax, which you must do within a month. Better still, get an accountant to do it.
19.    You should also have a lawyer “digitally sign” your articles of incorporation (Google for 電子定款), which will cost from 12,000 yen upwards. The alternative is to attach a 40,000 yen revenue stamp obtained from the Legal Affairs Bureau, but why pay the extra money? There is some disagreement about whether this is required, but it seems that whilst the company law does not require this stamp, the stamp tax law does.
Glossary
- Articles of incorporation (定款/teikan)      - A document setting out basic information about your company, such as its      purpose, address, directors, share distribution, etc.
- LLC application (合同会設立登記申込書) – A document setting out basic      information about your company in order to apply for incorporation.
- Declaration of capital deposit (出資金払込証明書) – Declares that an amount of money      has been transferred into the personal bank account designated to hold      startup capital. Each director should be listed and must stamp the      document with their personal inkan.
- Acceptance of responsibility as      company representative (就任承諾書) – A declaration by one director that they are the      representative (i.e. president) for the company. If you’re the only director then this      should of course be you.
- Decision on incorporation details (代表社員、本店所在地および資本金決定書) – Summary of      a meeting between directors stating office location, name of company      representative, and amount of startup      capital. I don’t think this document is actually a requirement, but      the Legal Affairs Bureau asked      for it so best to play safe.
- OCR application form () – A B5-sized piece of paper which you can get from the      Legal Affairs Bureau, on which      you print out the same details as on the LLC application document, but      formatted in a certain way so that it can be easily scanned into a      computer and optical character recognition (OCR) can turn it into a      computer document. Madness.
- Company inkan registration form – A form which you can get from the Legal Affairs Bureau to register your company inkan.
- Personal inkan registration      certificate – Proof that your personal inkan has been registered.      Available at your local ward office for a few hundred yen.
- Inkan (印鑑) – Also known as a hanko. A stamp      or seal that is used in place of a signature on documents. The company      inkan should be 18mm in diameter. Any      inkan shop will sell them, otherwise just Google for 印鑑 and you’ll find plenty of online shops. You only      need a single, round company inkan, 18cm in diameter, and they start from      7,000 yen.
- Legal Affairs Bureau (法務局/houmukyoku) – Bureaucratic government machine under the      Ministry of Justice. You can find your office’s local bureau at      houmukyoku.moj.go.jp/homu/static.
- Virtual office – Provides the facilities of an office, including mailing      address, receptionist, meeting rooms, etc., for a considerably reduced fee      compared to renting physical offices. Servcorp and Regus are the two big      ones, and a few others operate in Japan.
- Startup capital – Although this can in theory be one yen, it should in      practice be an amount “reasonable to operate your business.” I’ve no idea      how that’s assessed, given that you’re not required to show any operations      figures. The capital deposited by each director must be proportional to      their percentage ownership of the company. You can include in your startup      capital the 60,000 yen required to purchase the revenue stamp. Once you      have photocopied the bank book or printed out the online statement showing      the startup capital deposited, you can then withdraw that amount in order      to purchase the revenue stamp.
- Revenue stamp (収入印紙/Shuunyuuinshi) – A 60,000 yen stamp available from the Legal Affairs      Bureau or post offices, which is attached to your LLC application form and      covers the Bureau’s fee for incorporation.
- Evidence that startup capital has      been deposited – Take photocopies of front page      and inner page of the bank book for the account, with the startup capital deposit shown.      Shinsei Bank do not provide a bank book, but a printout of your online      activity statement and photocopies of the front and back of your cash card      should  suffice (check this with      your ward’s Legal Affairs Bureau,      as the situation may differ from ward to ward).
- Company inkan registration card      application form – A blue form available at the Legal Affairs Bureau. You should      complete it and return it when you return to the Legal Affairs Bureau, in exchange for a company inkan      registration card that you use when you want to purchase further inkan      registration certificates.
- Inkan registration certificate      application form – A brown form available at the Legal Affairs Bureau. You should      complete it and return it when you return to the Legal Affairs Bureau, in exchange for inkan registration      certificates (印鑑証明書).      You will need at least two certificates as they are used for various      purposes such as registering for corporation tax and opening a corporate      bank account. Each inkan registration certificate will cost 500 yen, which      you will need to pay by purchasing revenue stamps at the Legal Affairs Bureau.
- Incorporation certificate application form – A purple form available at the Legal Affairs Bureau. You should complete it and return it when you return to the Legal Affairs Bureau, in exchange for incorporation certificates (履歴事項全部証明書). You will need at least two certificates as they are used for various purposes such as registering for corporation tax and opening a corporate bank account. Each incorporation certificate will cost 1,000 yen, which you will need to pay by purchasing revenue stamps at the Legal Affairs Bureau.
 
