Whether you expect refund or not the process is pretty much similar -- I am assuming your desire for the ITIN for your wife ( who is and was a non-resident alien) is because you want to file MFJ. Note that you are a dual status taxpayer -- NRA ( Non-resiendt alien ) for the first part of the year i.e. till you met the susbtantial presence test sometime in early August and therefore only US sourced income is yaxed by the USA; the rest of the year you are a "resident for tax purposes" and your world income is subject to US taxes. Also if your wife agrees to file jointly with you ( Married Filing Joint) then her world income would also come under US perview. Generally, if she did not have any world income during her US stay and thereafter till the end of 2016, then filing joint with and ITIN may be advantegous for you.
The easiest way to file joint with a NRA spouse is to file a W-7 form ( Application for ITIN ) along with all the documents required and paperfile -- this means that she has to wet-sign the forms ( Fed-EX or DHL use is suggested ). This ITIN then is retroactively applied to 2016 return -- you need the ITIN solely for the purpose of filing MFJ. This essentially answers your Q1, Q2
Q3 -- you can perpare your return using MFJ and then if you find that you may have to pay some money in to the IRS ( you owe taxes , instead of a refund ) then you can use pay the extra amount along with your request for an extension, This will grant to time till Oct to file your return -- of course the sooner you file the return the sooner the ITIN will be issued.
Hope this answers all your needs -- if you have more , please consider commenting to this or start a new specific question
