I think that affidavit is the same one or similar to non-op. I doubt if you can get it back dated. Just an FYI, when your reg is suspended for no insurance, that just impacts the legality of driving it. If you simply don't insure the vehicle for a few years, you'll still be responsible for the back fees.
I think your best bet is to spend some time compiling all your paperwork you have so far, if you haven't already. Any receipts you've got, the CHP process you went through, etc. Whatever records you don't have, go back to the office that issued them, and for a small fee, you should be able to get copies. That way, you can take them to a new person at the DMV, with a giant folder of paperwork, covering all your bases, and showing that you did it the way they said, it just took a long time. The person may just go along with it, and follow the original plan, or they may cut you some slack on the fees, simply because they don't want to work through all the paperwork.
Sounds like you're fighting an uphill battle, Not saying its right, but ultimately, it comes down to what they say to do. If you don't, your truck doesn't get registered. Your job now is to make it as easy as possible for them to see that it really wasn't running, and you've really been trying to play by their rules. Even a printout from your insurance agent stating that your truck WAS NOT insured for the last two years may help.
