The information that can be requested is on the official form produced by the Virginia State Police. The statute says that they have the power to make up the form, so no one else can mess with the information required, other than to require fingerprints pursuant to a valid local ordinance. I tell people to fill out the form and politely ignore any requests for information beyond that. The clerks' offices are still required to produce the CHP within 45 days, even if they didn't get what they wanted.
Secondly, recognize that when you file your application, it's not just an application for a permit - it's a court case, with a case number and a filing date. Make two duplicate originals of the completed application, properly signed and such, and take both to the clerk's office in person along with the required payment. Tell the deputy assistant clerk in charge of sitting by the window that you want the second original file-stamped for your records. You have an absolute right to have that, so insist and escalate as necessary. That second, file-stamped original is your proof that you filed it on a particular day, along with the cash receipt!
Finally, you have an absolute right to file the application the way you want it filed. There is a statute that says that the clerks do not have discretion about whether to accept such things (there are exceptions for some documents that have to be notarized and such, but that mostly has to do with land records). The law says that if there's a problem with what you've filed, that problem has to be resolved by a judge, not the clerk. Feel free to tell 'em so.
Oh, and one other thing - the clock starts ticking on the day you actually show up to file the permit along with the filing fee. That's "day zero", however, not "day one". Since they don't have the right to refuse to accept it, all you have to do is drop it off with the filing fee, and that starts the clock. If you have some reason to think they'll ignore it, and not treat it as properly filed, you may want to bring a witness along with you just in case. Make sure your witness knows the contents of the application so he can truthfully testify that he recognizes the duplicate original as a true and correct copy of what you filed.