If I understand you properly, you are wondering why you're getting two different interpretations of the guidelines set forth. I think it has to do with the "line upon line, precept upon precept" thing. 
 
I read the Word of Wisdom and what I read tells me that God doesn't want me injuring my body by drinking harmful substances. I see that He cares about me and wants me to return to him. For me, the Word of Wisdom is one way to let me know that He cares about me. With that in mind, I make a point to refrain from drinking or eating anything that might hurt me. Why would I want to do so anyways, knowing that caffine and alcohol are bad for my health? 
 
That's what I get out of the Word of Wisdom. I included that here so you know where I'm coming from. 
 
 
Are walnuts bad for your health? I don't think so. The point is not the literal meaning of the exact words. The point is growing closer to God by obeying His commandments. So try to understand these commandments, listening to those authorities above you who probably know what they're talking about and are there to help, and do the best you can to follow His laws. I think that He knows you're doing the best you can, and He will probably forgive you for not being perfect. Also, *points to Phillip's fantastic explanation* He did a pretty good job of clarifying stuff. ^_^ 
 
Okay, now back to the original question by Robert. For starters, coffee is bad for your health. Yes? (That's been proved someplace by some scientist, can't find a link, sorry.) So why would you want to drink it? Why would God want you to drink it? What possible benefit could there be from putting such horrid substances in your body? I'm not talking short term. 
 
"Near beer"? Is that alcoholic drinks and wine? Same objections as regarding coffee, above. But I think you want to know what's "allowed". So, allowed. First off, the guidelines given to us by the Church are just that- guidelines. They're meant to protect us and help us, not trap us. They are breakable, but a heavy price is carried for breaking them. 
 
But that's slightly besides the point. Coffee and near-beer, as you put it, are not allowed because they are bad for your health and will bring you farther from God and closer to Satan. (Satan aka Lucifer aka the Devil, whatever you want to call him.) Plain and simple, that's the answer to your question, Robert. 
 
((Please note that I am not a Church authority and, while I will answer to the best of my ability, I am not perfect and have probably made a few mistakes in the above passage. Bear with me, please.))