OK, let's see. You asked about the sponsor's income: it's not that it's "irrelevant", it's just that there are no minimum income requirements to sponsor a spouse or dependent child. So, although it is pretty important that you have a job so you can show you're able to support those you are sponsoring, you don't have to make a certain amount of money. That's why CIC still requires sponsors to provide an Option C printout (so they know you are not on social assistance or in bankruptcy), and a letter from your employer. (See the sponsor's document checklist.)
Your wife being pregnant does not mean that you cannot file the application- and do at least most of the medical exam. What it does mean is that, until her Dr tells her it's safe, she cannot
complete the medical because she cannot get the chest xray done. The most expedient way to deal with this is to get the medical done without the xray, and complete the criminal clearances and the application forms and submit everything. CIC will process as much as possible, and then put the application in pending until they receive the results of the xray. When her Dr says it's safe to get the xray done, you'll be able to forward confirmation of that to CIC and they will request the results and finish with the file. There's info about this in
Section 11 of the DMP handbook.
Getting the photos should be easy if your wife is in Canada - anyplace that does passport photos can also do the immigration photos. There's Japan Camera, and even the photo studios within places like Sears and WalMart can do them. Just take the photo specification sheet from the CIC application package and they can cut the photos to spec.
As far as the Extension Application - I wouldn't risk it being returned to you over advice from a Call Centre agent that the fee will be waived! It could really screw up her status here - and Call Centre agents are notorious for giving out wrong information. It's only $75! The important thing is that the application has to be received by CIC BEFORE your wife's original status in Canada expires. You will need to be able to submit something that proves her entry date - which is the disadvantage you're at if they didn't stamp her passport. If she has an airline ticket stub or something of that nature, maybe even the Personal Inventory sheet if it's dated and signed by an IO, then go ahead and submit the extension so that it's received before six months is up. Be sure to include a copy of your marriage licence, and proof that you are filing an application for PR sponsorship. (Good proof is a photocopy - be sure it's marked COPY - of the receipt you get for paying the PR application fees). You should also submit proof that there is an available income to support her so there are no concerns that she will work illegally to support herself. If you don't have a way to prove her entry date, a trip back to the border for both of you - to get her a Visitor Record - is advisable. There's specific info on how to accomplish this at the
US2Canada website, under the "Visiting" tab. (Don't mention that she's already been in Canada for up to six months.)
Don't know where she's from but I suspect the States because of the no passport stamping thing. Please do yourselves a favour and file an outland application through Mississauga/Buffalo and get her permanent status as soon as possible with that baby coming.
P.S. Did they make you pay duty on her belongings coming in? That Personal Inventory sheet is supposed to be used when she lands so that she does not have to pay duty on declared belongings she's bringing in to Canada as a landing immigrant!