2) Even after she gets the waiver and becomes an H1, your sponsorship won't help her for 6-7 yrs. she will need to get GC on her own
Priority date for Family category 2A(spouses of GC holder) is dec 97. In aotherwords, while you may file I-130, you can't file I-485 till 2009 or so. But, as an H1 physician, an employment based GC will be pretty easy for her.
3) If she still has to go on with her J1, she cannot visit home anymore. It will bw tough proving non-immigrant intent when your hubby is a GC
This applies if she needs to get a new J1 stamp at the embassy for coming back to the US. Visas such as J1 B1 F1 are non-immigrant and the applicant needs to demonstrate strong ties to the home country to get it. If the spouse has a GC, it will be pretty tough to prove non-immigrant intent. H1 on the otherhand has 'dual intent' and cannot be refused if there is no fraud involved.