Agreed with mcl. Every program will be different, I expect most will wait for your transcript before offering an interview.
what if you only have step 1 score and CAF but no lor, should I wait till all my lor are in or just apply on 9/1?
People seem amazingly focused on applications submitted on 9/1. If you're an IMG, then it behooves you to get your app in early. Programs that take people outside the match tend to interview and try to fill earlier in the season, and getting your app in on time makes you look like you know what you are doing.
For AMG's, it really doesn't matter all that much. Programs/fields that are competitive will wait until later in the season so that applications are complete. Those that are not and hence might offer interviews earlier won't care if your app is in 9/1 or 10/15.
Bottom line:
1. IMG's are best served by having their apps in early. ECFMG isn't terribly speedy about scanning documents, so there are additional delays built into the system.
2. AMG's should probably have their apps in by 10/15 for most programs/fields, but honestly even apps in November would probably be fine.
3. If you know you want to apply to a program, then do so without worrying whether all of your information is available. Programs will wait on your application until it is "complete enough" to review (which each program can decide for themselves). Waiting until your application is complete does not really help.
4. The only exception to rule #3 I can think of is IMG's with an "important LOR" -- i.e. one from a US rotation. I would make sure that letter has been uploaded and is available before applying to programs, else you risk having your application reviewed without it (if, for example, you released 4 letters to a program, and 3 had been received, but not that "important" one).