What concerns do I need to look into when running a high current alternator?

Sound like you have considered many things. Since the OEM alternator wiring was most likely designed for a 40 to 60 amp system you will need to fix that. One way to do that would be to add a second cable to the 100 amp alternator with fuse and high current relay so it is powered only when in the accessory position. Since the 500W stereo is about 42 Amps at 12V you need to design wire size for more than that.

It is also a good idea to work over voltage drop issues on the original wiring and do the amp meter bypass modification. Without the engine running the feed will come from existing wiring. It would be best to beef up wire sizes, and limitations like bulkhead connector terminal ratings.

To run the 100 amp alternator may require 2 pulleys, so there may be work with that unless that already exists.