OK, in order, the 40 amp unit was keeping up the electrical system but was not really charging the batteries. 12.87 volts at the batteries.
Yes it's smaller.
The 40 amp unit came off of a mid to late 80's Colt.
The 90 amp unit provides 13.87 volts at the batteries. I used 8 gauge wire instead of the 10 that came in the Painless harness but it's still a long way back to the batteries.