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?