You have a bad ground or your runs of 0 gauge are too long or poor quality. Not all "0" gauge wire is the same, I found out the hard way. Lots of manufactures are selling something that is the equivalent of 4 gauge thickness and its copper plated aluminum (CCA) or not very pure OFC.
As you have stated, there are lots of people who use 90A alternators in the real world without much issue. I use a 75A alternator in one of my installs with 1200WRMS and rarely run my engine to charge the battery back up. //content.invisioncic.com/y282845/emoticons/wink.gif.608e3ea05f1a9f98611af0861652f8fb.gif I only charge when I have voltage dropping into the low 12's.