Great PA sent her back

I had all my papers sent back from Harrisburg saying that I needed a DR 123 from Florida, the state in which the sales tax was paid. I printed off a dr123 from FL, but its as if I was physically in FL, and has to be notarized as such. I never stepped foot in FL for the vehicle, so since they have sent it back, and giving me the run around, do I have to repay the full tax amount to PA, or can I use the "better" purchase amount.?

You did not say where you got the truck from but by your location as Central Pa. I will assume that it was here in Pa.
Your paid invoice from GL should show that you paid the 6% Pa sales tax and when you fill out the MV1 you show the tax credit as already paid. You will not have to pay the tax a second time.
The Fl dealer reassignment form would only be for the title transfer.

I picked the vehicle up in NJ, but the SF97 has a Florida address.

I picked up at truck in PA and got an FLA Title not an SF-97. I live in NJ. Here you need the FLA Title. No tax was collected and I have to pay that when I get go to register and get a plate. I like getting the title better then the SF-97; but I guess each state is different. I guess that is why GL gets the $60 bucks for doing the deal.
Good Luck