The formula for finding the number of combinations of k objects you can choose from a set of n objects is:
n! n_C_k = ---------- k!(n - k)!The formula for finding the number of permutations of size k taken from n objects is:
n! n_P_k = -------- (n - k)!But the formula for finding the number of permutations of size k taken from n objects when repeats are allowed is:
n_R_k = n ^ k
Now repeated runes in runewords are really combinations, not permutations, so the number we are interested in (n_R'_k) is a bit less than n_R_k. We don't really care which Feh rune goes in first when we make Feh-Feh, in a two-rune word, or Feh-Thor-Feh in a three-rune word. (But Feh-Thor-Feh is still different from Feh-Feh-Thor or Thor-Feh-Feh. General note, in the two rune case, n_R_k = n_R'_k.)
Misjy has 32 runes we can use in runewords. Just looking at two-rune words alone, n_C_k = 496, n_P_k = 992, but n_R'_k = 1028. Add in three-rune words and you have additional n_C_k = 4960 and n_P_k = 29760 and 29760 < n_R'_k < 32768. So you would need over 32700 lines in Runes.txt to cover just two-rune and three-rune words. (I'll leave it to the determined party to calculate the exact amount or for the four-rune, five-rune and six-rune cases.) Mind you, I haven't addressed the situation where a runeword does one thing in one group of equipment and something else in another, so there is a variable multiplier to consider. A program could do this easily enough (it is a little big for Excel), but keeping track of it would be most unholy.
Unfortunately, the observed limit for Runes.txt in v1.10 appears to be 4096 lines. (We would love to be proven wrong here. In v1.09, Kato was able to make almost 7500 words.) You could exceed that using just two-rune words if you have enough differences based on equipment!
Reference 1 Reference 2