Hey Pilothawk,
Where you from?
Keep it simple man! I'm doing the exact same thing as you, DIY stringing together lithium battery packs to run a 36v Minn Kota trolling motor on my bass boat. I suggest you keep it real simple and stay with LifePO4 tech, and build 12v batteries with 4 large square prismatic cells. They're simple to manage, connect and fix. The easy 54a low draw of that trolling motor is no problem. I'm planning on making 3 12v batteries to replace the group 27 FLA batteries and connecting them in SERIES, Lol. Easier to buy a 3 or 4 bank Lithium charger that way too and you can charge or jump start your dead crank battery for a sec from one of those 12v t/m batteries.
You can buy 4 new or used 3.2v LifePO4 cells and put them in series, get the 100a smart BMS Will recommended with bluetooth smartphone app for quick monitoring and do WAY better than FLA for hardly any more $$ and get 4x the life!
A 12v group 27 FLA battery may have a capacity of, say 80Ah, BUT, with FLA tech if you pull it down below 50%, voltage drops so low your t/m will barely run, AND it kills them real quick, as you've been doing. If 3 group 27's have been fine for you, then three 12v 50Ah LifePO4 packs will be fine because unlike FLA, you can use 100% of it's storage. Guys on bbcboard bass boat forums are doing exactly that, repl group 27 FLA's with 50Ah Lifepo's and getting BETTER runtime. That being said, it's best to NOT kill your lithium batteries every day either if you want them to last 10 years; work with an operating range from 80% to 40% and they could outlive you.
I'm overshooting and making 3 12v 75Ah batteries for the 36v trolling motor, but I may also switch to a 24v Garmin Force because its brushless motor is both more powerful and way more efficient than the Minn Kota armature. The same Garmin can be set to run at 24v or 36v, and 75Ah should be fine for long days fishing and which ever voltage I run. If you build 100Ah lifepo batteries, you'll be able to fish a couple big days no prob without charging, from what guys say.
As you probably already know, LifePO4 can last you over 10 years if you're careful. Don't treat them like FLA. Don't store them at 100%, store them at 50% AND disconnect them so they don't get accidentally drawn below 2.5v per cell. Do not overcharge. Do not draw them down below 2.5v per cell. Do not charge below freezing.
I'm doing it! I'm ordering cells from China here real soon. Trying to find good cases. I'm doing my engine starting battery too, but even bigger, 150Ah for headroom and fish finders. Lets do this!