I have a intermatic 104c which is the digital programmable dual poll single through timer. It will be wired for 240, it has six terminals on the bottom two line, two load, and two to power the timer. The manual shows a neutral and hot to power the timer, I'm a little comfused as to why I can't jump power from one of my line/inputs so as to avoid running two wires.

You can.
The clock mechanism is intended to be powered by the line side connections. It should actually be that way from the factory.

I have a intermatic 104c which is the digital programable dual poll single through timer. It will be wired for 240, it has six terminals on the bottom two line, two load, and two to power the timer. The manual shows a neutral and hot to power the timer, I'm alittle comfused as to why I can't jump power from one of my line/inputs so as to avoid running two wires.
I am going to wire it with just the 240 line and load and see if it switches, if not then add the neutral. Seems like as you said it should be prewired to power itself.

Confirm the clock is a 240v feed and not 120v. The ONLY reason the clock would require a neutral is if it was 120v. This would be odd though.