Legal Question in Immigration Law in New York

First, I have to ask if you have already discussed this with the Attorney who is handling the Labor Certification & I-140 on behalf of the petitioner?

Next, if your PD is current in June, you still have to make sure that the I-140 petitioner is willing to go forward with the case (meaning, the offer of employment is still valid at this time).

I also am curious as to why the H-1B extension was denied, as you are eligible for such if your I-140 has already been approved & your PD is pending.

As far as other options, besides filing for AOS in June or H-1B visa extension/change of employer,there is also the possibility of an F-1 if you plan on getting your PhD.

Keep in mind that if your wife is subject to the 2 yr foreign residency requirement, she'll need a release in order to be able to file for AOS based on your employment based case. Since you are now J-2, that release will probably also be required in order for you to adjust as the principal. I would highly recommend you discuss this with the Attorney who is handling her J-1 visa case &/or your J-2 visa change of status application &/or the Attorney who is handling your LC/I-140.