There is no specific order that the app and the transcripts or LORs have to be submitted. You can submit LORs and transcripts before submitting your app (bad idea, IMO), or you can submit your app and send in the LORs and transcripts later. Or submit your transcripts, then your app, then your LORs.
Or first your LORs, then app then transcripts...
...ad nauseum...
Again, it's best to submit your app as soon as possible and not worry about timing it to coincide with LORs or transcipts or grades or whatever.