Starting issue

Load test all the batteries after disconnecting them. Did NAPA do that? Also load test the alternator. Voltmeter on the alternator does not tell much. Alternator can produce voltage and be weak on amps, especially under load. You don't say if it turns over slowly but not fast enough to start, or if it clicks, or does nothing when you turn the key to try to start.
Voltage drop test between the batteries and starter.

 

I’d look at the ground from batteries to frame since you’re able to jump it at starter.

 

You can drive till you get down below 5 amps. ECM needs minimum of about 3 amps. Something is corroded or loose somewhere. What make Truck is it?

 

With 14.5 volts at the alternator and starter but only 13.3 volts at the batteries tells me you've most likely got a bad connection between the batteries and starter.

Run the engine and put one of your voltmeter leads on the starter positive stud and put the other lead at the battery positive post. Whatever you read on the meter is lost voltage. Do the same with the ground. One meter lead on the starter ground strap at the starter if it has one, if not then put it on the starter housing. Other lead to the battery negative post. Whatever voltage you read is lost voltage. Any loss over 0.5 volts on the positive and negative combined is considered unacceptable.

 

Alternator is fine. Cables or ground is the problem. Little wire from alternator may be shorting out, not sending a charge to batteries. On mine it runs to the starter, where it meets up with the 2 hots from battery. You could run a jumper cable from positive battery terminal to positive post on starter. If it works, you know the positive cables bad. Same with grounds. Starter to frame. Battery to frame. Probably have 2 positives running from batteries to starter. One of them may be chafed and rubbing on frame or battery box. Maybe just full of corrosion. What kind of truck is it? Freightliner?

 

Should that 0.5 V drop not be measured while cranking the engine?
Over O.5 amps on any cable period?

 

Cranking would be most accurate for sure. With the current draw from the starter that voltage drop will be higher than what you would see from the alternator supplying the amperage to maintain the batteries. I was just thinking it may be difficult for one person to check it while cranking if he didn't have leads he could clip on.

 

Jumping at the starter is only 1 wire.
pretty straightforward job. will isolate any cranking circuit issues.
or remove the starter and check it on the ground. hard in some trucks… yes.
but so is not having it running