Get a new lawyer. You can definitely do a round with different investors getting different share prices. At the very least, your lawyer can structure a Series A-1, A-2, A-3, each with a different share price, but otherwise being identical in terms and structure and everyone signing the same docs. Just make sure preferences are clear that the classes get liquidated pari pasu, if that's what you want.
No, it will not. I'm not sure what filing fees you are referring to. Your Schedule D with the SEC? There's not much else that needs to be filed. This can all be done in one 409A evaluation immediately after the financing.