1) Because I travlelled with expired AP, the CBP only give me 3 monthes on my port parole instead of 1 year for nomal AP so the expiration date for I-94 is 6/3/2010. As I'm not sure how this event will impact my I-485, does it mean I'm out of status after 6/3/201?
-Your status will be AOS after the parolee I-94 expires. You can stay in US legally with AOS
2) if my I-485 is rejected in future, will 6/3/2010 be the start point to calculate my days of out of status?
-You do not have a non-immigration status (e.g. H1, etc.) after you used AP, so you can not say you are out of status. If your I-485 is denied, your unlawyful presence will be counted from the date USCIS require you to leave U.S. in the denial notice.
3) Now I'm applying for a new AP. If the AP is approved, do I have to go out and re-enter US in order to get a new date on I-94?
-You do not need to do anything or get a new AP unless you want to travel again.