If there is any lesson here for the broader FT community it is that the fewer parties to a transaction, the better. When your transaction is directly with a carrier and things go wrong, the carrier will generally work to fix it if it can be fixed (not everything is fixable). Carriers are also regulated by DOT and while DOT is not the great hope that some on FT think it is, DOT can be of some assistance.
For complex matters where you lack expertise, a qualified TA can be very useful. Stick with someone you know and trust who comes highly recommended and does business in your neighborhood or office area. Those TA's charge fees and are worth the fees.
Unless an OTA or third-party opaque vendor is offering extraordinary savings, don't even think about it. While most people have no problems and it doesn't matter which booking channel they select, when things go wrong, a third-party is a problem. OTA's make their money on volume and spending time on the phone with you cuts margin. It also takes a level of expertise which most OTA agents simply lack.
OP was able to fix a problem in advance. When these problems occur enroute, they are harder and more costly. This isn't to suggest that there might not be a bargain to be had, but ask if it really is a bargain.