Hi Greg,
Currently there isn’t an option to wait for challenge file propagation (but DNS does uses pauses to allow for DNS challenge propagation).
In your case I’d suggest DNS validation (using v4 of the app) is probably going to be easier, as any server (or even your desktop machine) can perform the renewal, then it’s a case of distributing your certificate as required once it’s renewed (we don’t support Central Cert Store directly yet but it’s likely in the near future and achievable with custom post-request scripting).