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You should take a look at 11. Austin, M.P., Williams, O.& Belbin, L.(1981). Grassland dynamics under sheep grazing in an Australian Mediterranean type Climate. Vegetatio 47, 201-211. This gives you an idea on how you could analyze temporal and disturbance factors in ‘noisy’ datasets.

If there are independent environmental/disturbance factors, then it is possible that more than 3d is required for the ordination. But an overlaid MST will also give a good indication of this. See my notes on it.

I would never publish an (MDS) ordination result without the stress value (or variance in a PCA/PCoA).

If you have very disjunct communities, then ordination is difficult. Take a look at the histogram of association measures and see the notes on this in the help. It will tell you if there are disjunctions. If there are, then there is a strong case for independent analysis of each disjunct group. BTW: Disjunctions = high stress.