When trying to convert your OTU table to txt format using biom convert, the script fails-both with biom 1.0 and with 2.1.3 (current version). Therefore, it seems that your OTU table is not formatted correctly. What I would recommend is that you recreate it, and avoid opening it in anything except for a plain text editor. At this point, run the biom summarize-table command on your table to ensure it is in the correct format-if it isn't, that script will not work. Then, once you have an OTU table that will work, you can work on comparing your OTU table/mapping file/tree files to make sure the SampleIDs match between the mapping file and OTU table, and that the tree tips and OTU IDs in the OTU table match up (using a custom script here: https://gist.github.com/walterst/3144b1401fbda7bab464). Although you replaced the underscores with periods, it still doesn't look like your OTU IDs and tree tip IDs match up. For example, in seqs_new.tre, the tips look like this: OTU.10331;size=2; where the OTU ID in the OTU table is OTU.10331. The mismatch is even more apparent in seqsaligned.tre, where the tips look like this: seq_107. It's really important that the aligned fasta file you use for tree building has labels that match your OTU IDs, and that the output tree has tips that match these same OTU IDs, otherwise QIIME won't be able to connect the tree data to the OTU table.
Hope this helps!