I'm going to guess you don't have the dual alternator setup.

Take it to a battery shop and disconnect both batteries and test them one by one. If they test out good, check the charging system. Unless you have a dual alternator setup (probably not), I am going to suggest you take out the alternator and have it tested. When you untension the belt, spin the alternator. It should be on the top left part of the engine. If it drags at all or makes noise, get a new one. If it is fine, take it out for testing to make sure it does give the current you need. Since you can glow and start it, I am leaning more towards charging system.

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