The 3.5mm IR port on Denon receivers should operate ANY zones, not just 2 and/or 3. This may be different on the 05 series, but when I installed a 2007 model, it operates the Main and Zone 2 commands.
You may be in a situation where the previous owner removed somehting that would keep the IR from working. If there's no wall wart for power or no module for accepting the IR receiver's input and plugging the emitters into it, you'll need to replace them. Also, some IR receivers son't work well, if at all, when there's a lot of other IR sources, like direct sunlight, Compact Florescent bulbs and plasma TVs. I have seen regular light bulbs cause IR codes to be blocked.