Here are the charts for increases of transposed periodic ngrams resulting from symbol merges, at this new link:
http://zodiackillerciphers.com/symbol-m ... transpose/The
previous link still shows the untransposed periodic ngram data if you want to compare them.
Both links include 5-grams now.
Select "shuffle sigma" in the sort by dropdown to view the more significant spikes in the data.
Only one pair of symbols, "(W", produces an increase in transposed 5-grams when merged. Interestingly, the 5-grams appear in the same columns, at transposed period 68 which is a multiple of 17:
(I think that is the equivalent of untransposed period 5)
The same 5-grams appear at periods 69 and 70:


I'm still puzzled about the significance of this. Maybe these are just phantoms. It may be related to your earlier question, Jarlve -- if we are already looking at bigram anomalies at certain periods, then formation of larger-order ngrams might be more likely since there are more building blocks lying around.
And, more generally: Wouldn't we be seeing more convincing spikes if we were merging correctly selected pairs of symbols to form homophones? I.e., newly forming bigrams should be appearing at the anomalous periods. Maybe it's not sufficient to merge a single set of symbol pairs together at a time. We might need to expand the experiment to merge more than two symbols together, or even to consider more than one homophone at once (k sets of symbols, where each set contains m symbols). I'm planning to move away from this exploration for the moment though because I need to work on the cipher type identifier.