You are not at all anywhere near being overstocked in a 55g.
The rubberlip pleco is likely Chaetostoma sp. (L402), check the photos here:
This one gets 5-6 inches; some other species can reach 10+ inches. Pleco are waste factories, though one of these small ones in a 55g can't be the reason for such high nitrates, given your water changes and substrate cleaning described.
Check the tap water, this is important; knowing the nitrates (partially or perhaps totally) are in the source water is significant to dealing with this.
Wood will be OK for the pleco and shouldn't affect water chemistry much. However, we need to know the GH, KH and pH of your tap water; get this from the municipal water supply people, probably on their website, or call them. Coral will dissolve slowly and increase GH and pH, which may be no issue (you have livebearers that need moderately hard water with a basic (= above 7) pH) but we need to know the source water data to determine if this will or won't matter. The pH is 8.2 you said in the tank, and if we can lower this a tad (for the loaches) it wouldn't hurt, but I am not suggesting major water fiddling, just possibly removing the coral. Let's see the numbers first.
You can test tap water pH with your kit, but be sure to out-gas the CO2 first. Do this by vigorously shaking some fresh tap water before testing, or letting it sit out overnight.
It is quite amazing how beneficial a water change is. Whenever i see possible trouble, one of the first things I do (after running some water tests) is to do a major water change. I doubt there is a situation where this is not going to benefit. Fish are so closely tied to the water chemistry, much more significantly than any land animal breathing air.
Byron Hosking, BMus, MA
Vancouver, BC, Canada
Something we all need to remember: The fish you've acquired was quite happy not being owned by you, minding its own business. If you’re going to take it under your wing then you’re responsible for it. Every aspect of its life is under your control, from water quality and temperature to swimming space. [Nathan Hill in PFK]