Is having elaborate metaphors a bad thing in a short story (for the purposes of the story being accepted by a magazine)? How can I know if my metaphors are too elaborate?
Most of your metaphors do seem a bit confusing. Your first example compares parallel rays of sunlight to entrails, but entrails aren't parallel. Your second example compares newly formed clouds to transparent glass, but even the wispiest of clouds are far from transparent, they are opaque at best. Your third example "exhibitionist, twilight colors" brings to mind Ray Stevens streaking across a basketball court rather than the romantic setting you probably had in mind.
Th last one is fine. A crescent moon piercing the night makes sense, doesn't contradict itself and I can visualize it perfectly.
The problem with the others may be that you are trying to force them in, or not visualizing them well enough to properly portray them. Don't use metaphors just for the sake of using metaphors, they should be used to create an image in your readers head that they can relate to, thus taking your description from your words into Their heads. I can not relate to rays of light looking like entrails. But I could relate them to ribbons, or rivers or long brushstrokes.
Close your eyes and picture your setting. What does it look like? What does it remind you of? If you were describing it to someone who could not see it, how would you make them understand what it looked like?
Also, you should consider deleting about 90% of your adjectives. This is what's making your writing long winded and overly descriptive. To describe you beams of light as glowing, parallel and lemon colored is more than your reader needs or wants to know. take it easy on them, don't give them so much to process all at once.
I read your question before your examples were edited out, and would like to comment on them a bit, but I won't. It wouldn't be fair to the question as it is now. So, to address your current question of 'is using elaborate metaphors a bad thing' my answer is: No, not inherently. BUT you have to do it carefully to pull it off. So how do you know if you're doing it well? Here are some things I think you should look out for when writing your own stories and are thinking of putting in metaphors.
First, does the metaphor have any meaning? By this, I mean does it paint a picture, or are you only using it because it sounds nice. If it sounds nice, but gives absolutely no hint of an image or emotion to the reader and they just end up sitting there without a clue what your saying, then I believe it has failed as a metaphor. Read over your metaphors and ask yourself if you can actually visualise any of them. As a good example of a metaphor, the opening to The Highwayman by Alfred Noyes has (in my opinion) some of the best use of metaphors in written work. Can wind really be 'a torrent of darkness', or the moon a literal 'ghostly galleon'? Of course not, but it paints an image, one of gusty winds at night blowing along the hills, and the moon big and bright floating among the clouds. To use one of your (now deleted) metaphors as a not-so-good example, you used the line 'Beams of glowing light emanated from the windows in parallel rays, their lemon colored entrails spilling out over the chestnut lined pews of the monastery.' Here, 'lemon colored entrails' is a metaphor. But does it paint a picture of light spilling into a room? I don't think it does. From what I know of anatomy, light does not 'spill' in the same way as a gutted animal or human's entrails would. Here, you'd be much better off just saying 'Beams of glowing light emanated from the windows in parallel rays, spilling onto the chestnut pews of the monastery.'
Second, if your metaphors are painting pictures successfully, the next question is whether you're using them TOO MUCH. A metaphor here and there can be very powerful tools, but using them to describe everything that each character sees, thinks and feels, as well in almost every paragraph of narration, is far too much. A reader may very quickly get sick of reading and just want to scream 'Just tell it to me straight already!'. Moderation is key.
And lastly, keep in mind that prose is not poetry. There's a reason I used The Highwayman as an example of well done metaphors. I think metaphors are much better suited to poetry. Perhaps you'd be better off learning how to write well constructed poetry that could accomodate your flowery writing style. If you really do want to keep writing short stories and novels, remember: Does the metaphor having meaning, and are you using them too much?