Well, at least you know what the problem is now. Its not the end of the world to fix, but it will be a pain. The injector pump can only be bolted to the drive gear one way, so thats not something that can ever get out of time. However, the gear can get out of time with the camshaft gear if its removed. Practically guaranteed actually even if you brought it to TDC.
Worst case senario, you will have to remove the water pump and then remove the front engine cover to expose the timing marks of the gears.
Best case senario, you will have to get a really small, flat piece of polished metal like a really good butter knife or perhaps a thin piece of mirror to peer down into the front of the engine so you will be able to find the timing mark. The timing mark is on the front face of the gear, and there is no mark on the outer circumference. Good lighting is requred for this
Start by bringing the engine to TDC like you did before and start looking for that mark as described (shaped like a small "Y"). If you can't find it, roll the engine over one full turn and look again. Once you find it place the gear in position, then install the gear cover. Do not attempt to install the gear, cover and injector pump as one assembly.
The injector pump is intended to be removed and installed injector lines and all without disturbing the gear cover. It is a little tricky, but there is enough room (the designed it with this problem in mind).
Good luck.