mafft | Align multiple amino acid or nucleotide sequences

I have three files, they look like this:

I have some data that describes an ordered set of discrete events (or states). There are 34 possible states, which may occur in any order and may repeat. Each sequence of events can contain any number of events, and crucially there are more than 2 sequences of events. My eventual aim is to cluster these sequences into similar subsets, but my hunch is that this cannot be meaningful unless these sequences are aligned such that equivalent events occupy the same position in all sequences.

I'm very familiar with multiple alignment of biological sequences, but all the software I've come across for this (MUSCLE, MAFFT, T-COFFEE, Clustal*, etc) require DNA, RNA or AA sequences, and I have more states than any of these, so I can't get them to work.

I've found various implementations of the pairwise alignment algorithms such as Needleman-Wunsch in R, but so far haven't come across any generic (non-biological) implementations of any multiple sequence alignment algorithms.

For example, say my data looks like this:

I've been attempting to use the MAFFT command line tool as a means to identify coding regions within a genome. My general process is to align the amino acid consensus sequence of a gene to a translated reading frame of a target sequence. My method has been largely successful. However, I've noticed some peculiar alignments which will unfortunately impede my annotation method. The following is one such example (Note - I've also included a pairwise alignment from the Pairwise2 Biopython module to demonstrate my desired output. Unfortunately, the computation time for Pairwise2 is nearly 20 times slower than MAFFT command line):

I've been trying to use the Mafft alignment tool from Bio.Align.Applications. Currently, I've had success writing my sequence information out to temporary text files that are then read by MafftCommandline(). However, I'd like to avoid redundant steps as much as possible, so I've been trying to write to a memory file instead using io.StringIO(). This is where I've been having problems. I can't get MafftCommandline() to read internal files made by io.StringIO(). I've confirmed that the internal files are compatible with functions such as AlignIO.read(). The following is my test code:

I am using mafft from the biopython package to align my sequences:

I am interested in running mafft from biopython. It works fine (code below).