Being that you have a 2008 I would assume you have at a minimal a surepower 1315 , or even possibly you hit the cut in of the Blue Sea 7622. The voltage of 13.28 is low, the surepower won't connect until it see's a minimum of 13.2 +/- 2%. Depending on where you are reading the 13.28, it may not be seeing 13.2 at the surepower.
If you have the bluesea 7622 the the connect voltage is 13.0 volts after 90 secs, again depending where the voltage being read it to may not be seeing the correct voltage. It could also be possible that someone used the lock out knob on the ACR especially since they were doing major work.
I would also question the output of the new alternator.
Another possible issue is if you have the Surepower, there would be a good chance that you are seeing a common problem of high contact resistance. In this case you would be able to here the unit connect, but still not really pass any current over the interior relay terminals.
Contact resistance build up is possible in the Blue Sea ACR, but not as prevalent as the surepower.
If you identify the Separator/Acr/Isolator you have we could give you some more specif things to look at.
2004 E350 EB V10 E/PH 2WD