The key typically stays in the slot in the pump. Just be careful to try to keep it centered when removing it.
There's a timing pin just next to the pump. It's spring loaded, it will only drop into the timing hole when the engine is at TDC. Just bar the engine over by hand till you get to the point that the pin will drop into the slot. Keep a bit of finger pressure on the pin as you bar the engine to feel when the slot comes around. As far as the pump, if you're taking it to a diesel shop, it will be returned locked down and at TDC, so it's a no brainer. Match mark the housing/engine so it can be re-mounted in the same position. If you're having the pump rebuilt, they may blast the paint off, so make the mark with a punch or small chisel.
If the only symptom is a leaking throttle/fuel shutoff shaft(s), there's a kit available to replace the o-ring seals on the shaft(s), you need to remove the top of the throttle housing. There are springs and parts under tension under that cover that must be carefully handled and returned to the exact position you found them. But it can be done in place. I've done it successfully; tedious, but do-able.
The CAV pumps typically go long hours without needing rebuild- (<6,000) so re-sealing the shafts might be all that's needed, but any decent injector shop should be able to handle a rebuild. Expect to pay in the $800 range for that. If you're going to have the pump rebuilt, pull the injectors and take with to have cleaned and tested. You don't indicate hours, Cummins recommends 2000 hrs for injector service, some of the Cummins gurus say that they can go much longer unless there are symptoms.