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Welcome to APC. I hope you'll find lots of good advice here. I did. I was a lurker a long time before posting questions too.

Plants and fish in nature are often subject to very, very cloudy water. Storms kick up lots of sediment and most fish don't even seem to notice. I do pretty significant re-scapes in my bigger tanks all of the time. I usually uproot the plants, remove hardscape items, and give the gravel a good vacuuming. LOTS of debris gets stirred up - so much that I sometimes can't see what I'm doing. It's always gone by the following day though. Some of it will eventually settle out on the plants. A little swish the next day will clean the leaves off again.

Unless I physically relocate the tank, I never remove the fish. Netting and transferring them is almost always more stressful than working around them. Leave them a little cover and they'll find places to hang out while you work. If you do decide to remove them, they can live quite happily for several weeks in a large tupperware bin, a clean garbage can, or just about anything else. Before you got them, your fish went through some pretty tough environments.

Like you said, aquascaping a narrow tank is difficult. If you are planning a major re-do, you might want to consider buying a different size aquarium. Once you have everything set up, the actual cost of the glass box is only a small part of the total. If you stick with a 48" length you can probalby re-use your lighting and much of the original equipment. The first tank would make a good quarantine setup, growout tank, or plant farm.

If you're stuck with the original setup, you can use a few tricks. You'll want to focus on front to back sightlines, leaving open space in areas to give it a sense of depth. Don't let anything touch the front glass. Focus on developing the forground and midground. Taller species are easy and will quickly overtake the scenery. Use them sparingly.

Unless they're truly overstocked, moderately or heavily planted tanks don't need to cycle. The plants will consume available ammonia long before it ever becomes toxic to the fish.
 
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