> Finished residency on H-1B and am in the middle of fellowship on J-1.
Almost there and then lost everything over a fellowship. The system is so stupid.
> If I get an HSPA waiver, can I join it considering that I would have
> only 3 years of H-1B visa from my 6 year quota left??
You only need 3 years in the HPSA on H1b in order to be able to convert to a green-card.
If you manage to get an immigration case filed during your waiver job, you can get 7th year and 8th year extensions on the H1b based on that.
Your options for filing an immigration case are the following:
#1 If you practice in a HPSA under the Conrad, ARC, DRA, HHS program:
a) you can file an I140 NIW based on the 'alien physician in underserved area' clause. No publications needed, just a letter from the state department of health stating that your continued practice is in the public interest. If you want to adjust under this I140, you need to complete 5 years in the HPSA and file paperwork to demonstrate your full-time practice. After you file the paperwork, the service takes its sweet time to approve you GC.
(++) high success rate, not bound to employer after the 3 years. You can establish your own office, as long as you stay in a HPSA/MUA and maintain state DOH support.
(--) You are stuck working on EAD for a long time, your travel is impaired by the need for an AP document. Every year you have the nailbiter of hoping to get your EAD renewal in time.
b) you get your waiver employer to file an LC and I140 for you. Now, this means you will be stuck with them past the initial 3 years. You can continue working with them either on H1b extensions or using an EAD. Some state Conrad programs prohibit the employer from sponsoring you for immigation until you have served 2 of the 3 years, they know that if you get a late start, you will be stuck in the HPSA far longer than the 3 years.
(++) if your timing is right, you can get your GC 3 years and 6 weeks after you start your waiver job.
(--) you are employer dependent. Believe me, physician practices are the most ruthless slavedrivers. Practices every sweatshop owner would go to jail for are normal. If you hand them the big stick of your immigration case, you are completely at their mercy.
#2 If you get your waiver job through the VA you have two options:
a) NIW through the VA. It is similar to #1 a , the difference is that the VA files the paperwork. Sometimes they play dirty tricks and don't file the paperwork in time in order to strongarm physicians into staying a year or two longer than they anticipated.
(big ++) these NIW petitions from the VA have a 100% success rate, it's the goverment petitioning the goverment, go figure
(--) You work for the same goverment that screwed you over with the J1 in the first place. Your income is limited to the VA payscale, if you are fellowship trained you take quite a hit for the addional years you have to stick with them.
b) NIW self-petitioned. 'Plain vanilla' NIW without the any VA or HPSA aspect. You just write a fancy petition that convinces them that it is in the national interest to waive the labor cert. This is where the publications come in, a strong university to back you for this is key. I know someone who got his GC this way while doing his waiver job with the VA. (problematic as the success of this type of NIW petitions is far from secure)
c) Labor cert based I140 through a practice that intends to employ you after your bonded servitude with the goverment is over. (the VA doesn't file LC's from what I know) Similar caveats as under #1b. Situation is somewhat better as you can go for consular processing and enter the country on an immigrant visa. By avoiding the AOS process altogether, your employer dependency is limited to a 6 month period of 'intent to be employed' period after you enter the country on your immigrant visa.
Oh, and before I forget it: Be very wary of your own countrymen. The person 'helping you out' might be the one who rats you out to the goverment if you fail to accept his pay cut to $60k
Good luck !
(just my 5 cents. I am a doctor, not a lawyer. The stuff I said here is based on my limited experience, on the experience of a couple of folks around me. )