1) Begin from 9/29, if my I-129 can't reach the USCIS center, what status I am in then?
-Your status is OK because your current employer needs to take some time to cncel your H1, so USCIS can not tell whether you is laid off or not (USCIS can not tell this from your paycheck also).
Am I legal if I just stay in the USA?
-You are lawful present until your I-94 expires even if USCIS cancel your old H1 status and you do not get the new H1 status.
2) If I-129 will be filed after 9/29, should I use premium process (I need to pay it by myself)?
-I do not think you need to do that.
3) After I get the receipt notice of the I-129,
Can I work for the new employer legally?
Or I just start work immediately when I-129 mailed out? Since there will be about 1 week mailing process for me to get the notice.
-You had better wait for the check is cashed (ask your new employer to find it out from the bank if the filing fee is paid by the employer) or getting the receipt and then, you can work.
4) If my requested H1B get approved, but without new 1-94, And I worked during the waiting period for the approval,
Can I get paid legally?
-Yes.
Will the employer get any trouble?
-No.