Will my application be rejected if either of us are HIV positive?

The HIV status of the Australian partner is not taken into consideration.

If the applicant knows he is HIV positive then a "Health Care Waiver" should be made as part of the application. Seek advice from AFAO. See the Health Criteria and HIV section.

There have been many changes to the Migration Law in Australia. I applied before these changes came into effect will I have to meet the new criteria?

The regulations and law which affect your application will be the law applying at the time you made the application. Any changes usually only affect applications made after the date of the changes.