Righto.
The e at the end of most words is quite simple. By starting with Ser and Estar you kinda took a dive in at the deep-end. Since, in the present it's Soy Eres Es Somos Sois Son, and Estoy Estas Esta Estamos Estais Estan - none of them end in an e.
Regular present tense verbs ending in -ir and -er tend to follow the same pattern in the present tense, with a few having stem changes (like Conducir becomes Conduzco, but it still ends in -o). So, you end up with "-O -Es -E -Emos -Eis -En", right?
So, we'll take comer:
you have "Como" [say it as you see it Co-Mo], Comes [Co-Mess] Come [Co-may] Comimos [Com-e-mos: pronunce your e there as in in e in "be"] Comeis [Com-ay-ss] Comen [Again, say as you see: Co-men].
And it'll be the same when you get to the subjunctive of regular -ar verbs. The third person, and first person, singulars will end in that "e". Which, simply, should be pronounced "ay". I can't think of a place where it doesn't exactly do that...even é tends to sound like that, with just a little more stress on it [which is good to know for those harder tenses later on, cause it pops up a lot].
Sorry about earlier. I thought it would have been a kick in the right direction, but, obviously you're doing it all off your own back and cramming the old grammar sans audio help. Kudos to you, as that's quite hardcore.
If you need any more help on pronunciation or anything, there's always the Spanish Society. We don't bite. And all the Spanish speakers are only a PM away - I'd rather see someone succeed at a language through getting as much help as they possibly can, than getting them to struggle on through.