If you plan on doing the big three just lay new wires.. no need to replace the old ones.. just double down with new ones. Electricity will take the path a least resistance anyway..
1) Bat to ground, easiest, just run a wire from the battery to the frame.. make a hole if needed in frame.. be sure you sand down to bare metal and all for get conductivity..
2) Engine to frame, Run a wire from the body of the alternator(not the + post) to the frame.. pretty simple as well.. I think you wanna use a different post then the Bat to frame but i'm not to sure if that really matters..
3) + from ALT, Run a wire from the positive post on the alternator to the fuse box and then to the battery.. follow the original wiring cept don't worry about going through the starter.. just go from the Alt the to fuse box then to the battery..
and on a side note I haven't done this with my D.. only on my neon.. and it worked out just fine..