Alright, so I've got a bit of a conundrum, so I'd like to ask those of you who've done the rail pass thing before . . .

did you have to present your passport or ID each time you used one of the rail-pass-based tickets?

No.

You will purchase a Rail Pass voucher before you enter Japan. After you get there, you will exchange the voucher for the actual Pass. At that time you will be asked to show your passport and to verify the exact dates you want the Pass to be valid. Once you have the Rail Pass, you can just walk through the manned gates beside the ticket wickets at each station and walk onto trains to use unreserved seating. If you choose to use the Pass to make seat reservations, you will just show the Pass when you make those reservations. Your passport number is on the Pass.

Of course, if JR personnel have reason to think someone is fraudulently using the Pass, such as someone other than the individual named on the Pass, they have the right to ask for id but I have never had that happen.

As abmj-jr stated, it would be highly unusual for you to be asked to show your passport in conjunction with the use of a JR pass at a station or aboard a train, although they have the right to do so at any point.

But, since foreigners are required to have their passport on their person at all times while in Japan anyway, I don't see what the "conundrum" is. Unless, of course, you have an intent to defraud.

The op orginally had more info in his post
 

It was something about a visa because the op was teaching English in japan and I beleIeve was already in japan. Assuming that it is legal to use a rail pass with this kind of visa I think he is ok having somebody in USA buy 2 rail passes and join him there to travel on the pass.

In this case, the OP is likely NOT eligible to use the Pass as he/she probably is on a visa status other than Temporary Visitor. I don't think JR would even exchange the voucher.

That Is critical information to the OP's question that was apparently removed by a mod. :(

It's NOT legal. There is one and only status for foreigners that is allowed to use the JR Pass: "Temporary Visitor." If someone is in Japan and working (legally) as an English teacher, then their visa status is going to be other than Temporary Visitor, and thus are ineligible for a rail pass.

Setting aside for a moment the issue of it not being proper for the OP to use a rail pass, there's also the issue of whether or not you could actually accomplish it. If the OP had a friend coming in that would NOT be traveling with them, then it's probable that they'd get away with it. But if the OP and the "Temporary Visitor" friend plan to travel together, there's no way that the friend is going to be able to activate two exchange orders for two passes with simultaneous validity during the same transaction. What is unknown (at least to me) is whether the friend could activate each pass separately (at separate times and JR offices) for simultaneous validity. It all depends on whether the passport number is entered into a JR computer at the time the exchange order is processed - if so, then it's probable that they'll catch this situation even if the friend attempts the exchanges at different times.

FWIW, the exchange order I have purchased in the past did not have passport number. It was in person at a JTB office, so they did take my passport to make sure the names match. I'd imagine there will be difficulty exchanging the pass if the names on the passport and the exchange order do not match.

On the actual pass itself, the bearer's name and passport number were hand written by a clerk during the exchange. I think the clerk also checked the visa status at this time, but I don't know if this information was entered into a computer.

1. passport stamp must show "temporary visitor" (i.e.90 days stay) to use rail pass
2. exchange order must be purchased and dated prior to arrival in Japan. I tried to get someone to buy a pass back home while I was already in japan on the 90 days temporary stamp but they wouldn't sell it.

I've been asked to show it on occasion- I think in Tokyo Station. Its rare but not rare enough that you should not take your passport with you.

If you have a visa that lets you stay in Japan more than 90 days (work, culture, student, spousal, permanent resident), your best bet for saving money on train travel is excursion tickets (shuuyuuken).

Their availability changes monthly, so you have to either consult the monthly JR schedule (available in most bookstores) if you read Japanese or have a Japanese friend do it for you. Basically, a shuuyuuken gives you round trip transportation to your destination along with a given number of days of travel within your destination area. For example, there's usually a Kansai-area ticket for Tokyo residents.

Some of the private railways have excursion tickets as well.

None of these are as good a deal as the JR Pass, but there's not a lot you can do about it.