When does a plan need to make an application for an determination letter regarding initial qualification status under the new staggered remedial amendment periods of Rev. Proc. 2005-66? May the plan wait to file for an initial determination until the first cycle corresponding to the plan sponsor's EIN? Or does the plan need to file for initial qualification immediately, and then re-file in the first cycle corresponding to the plan sponsor's EIN?

A plan rarely needs to file. If your new plan is an EGTRRA document and thus takes into account the items on the Cumulative List, you can choose to file, but you will be an off-cycle filer and at the bottom of the review list. Since you have retroactive reliance, I can't see too many reasons for not wanting to wait.