Got the pump turned to the original position that the old one was in and fixed a leaking injection line. Now the truck is giving me codes:

DTC 18 - Pump Cam Reference Pulse Error

and

DTC 35 - Injection Pulse Width Error (Time Short)

and the truck seems to be cutting out when WOT after ~2400 rpm. Any ideas on what could be going on?

How often is this DTC coming up? Have you reset it after? I would expect to see a few codes as the air passes the system. Have you checked the supply side of the pump for pressure or leaks?

The thing is throwing the codes every time I start it. I've cleared them out and then they are right back. Hard to start and lots of black smoke when getting into it. Could the timing be that far off?

I would help to look at the timing on a scanner, 12 pin or 16 pin ALDLl?

Symptoms are retarded timing, possibly from bad connection to Optic Sensor - oxidized connector, broken wiring, etc.
Recheck all the Inj Pump connections, also including the separate three-wire connector for the Crank Position Sensor, down front driver-side timing cover.

Disconnect OS, restart, engine will be in 'limp\backup' mode - will hard\long start, but let it run for 30mins like that, will clear pump and injector pipes, should clear up the DTC-35, which can be from air bubbles in the IP .
Then compare symptoms, which will be long start, low power low response - will give all the Optic Sensor DTC's, but ignore them for now.

Kill engine, re-connect OS, restart engine, see what symptoms still occur.