Hopefully you can still qualify for one of the programming discounts with a purchased unit.
The D1000 will receive all national programming in the "standard packages" on 110/119/129. The only reason to add another dish would be if you wanted some special programming, like internationals, or if your 129 signal is too low to be reliable. In that case quite a few folks in this forum have had better luck by optimizing a second dish for 129 or aiming it to 61.5. So make sure you hold onto your D500 just in case! Actually, you might just want to keep the D500 as-is on 110/119 and add another D300 or D500 for just that third sat. slot, whichever one you choose. You'll also have to consider the LNBs and switch. Claude at the DishStore can help you sort it all out.
Re: down-converted channels on TV2 - that certainly works for all the sat. HD channels. I can't remember if I ever checked it on the single OTA HD channel I can get but I believe that should work as well. If you're watching on a 4:3 TV you might want to tweak the zoom (* button) to choose the best fit for any given program...