That is strange, I didnt play Otomo yet but i do not have issues with the navies, it works fine for me. Maybe you have some traces of other mods that conflict perhaps? They don't move on the campaign map or during battles? I have played 2 campaigns so far and only crashed once.
Maybe you should reinstall a clean copy of shogun2 and then download the mod on steam and enable the modules in the right order, i did that and it works like a charm. The only issue i had was in the Ise region, there is a narrow pass that only leaves room for one agent or army to go through so the crash happened there when i sieged with one army with a general behind me in that spot and retreated the siege to see what happens. It can also happen in Omi perhaps near the farms close to Echizen.
I really hope Weierstrass is still working on this amazing mod, I would really love to see new clans playable, I love this period of history and to have a clan like Saito playable for example would be awesome. Somehow it is one of the clans that has not been made justice in this game or in any mod.
Their warriors were truly a force to be reckoned with, Oda Nobunaga drew many of their retainers in his army (Akechi Mitsuhide, Ando Morinari, Fuwa Mitsuharu, Inaba Ittetsu, Mori Yoshinari etc..) alongside their famed samurais absorbed in his armies. The province of Mino ruled by Saito Dosan before the start date, the man who started as a monk then a merchant and who ultimately became a daymio of Mino (what a destiny..) and made the province quite prosperous which attracted men of valor, his armies were feared in the region. To give a few anecdotes, Nobuhide, the father of Nobunaga was defeated by Dosan's army in 1547 before winning a pyrrhic victory later on, Nobunaga himself was defeated by Saito Yoshitatsu's army after Dosan's death when trying to avenge him with all his might. This wasnt because Yoshitatsu was a military genius but essentially due to the high value of the Mino warriors and the skill of their generals. The only reason why Nobunaga could conquer Mino after Yoshitatsu's death was because of massive defections of Mino retainers and samurais to the Oda army, otherwise it would definitely not be possible at all. In fact without the Mino samurais in his army, it is arguable that Nobunaga would not have been able to march to Kyoto defeating several clans in the process, and would not have been able to defeat the Asai-Asakura ( with the considerable help of the Tokugawa allies) at Anegawa. The Mino samurais were that fiercesome in battle, people know about the Takeda samurais, the Shimazu warriors, the Echigo warriors , Mikawa samurais etc, but the Mino samurais are often overlooked even though they were instrumental in Nobunaga's army and arguably the strongest warriors in the region. In the context of the mod it means that the Saito clan could have a bonus for yari samurais and/or mounted samurais perhaps a bonus for trade. Trade cause of one of the reasons Nobunaga did his best to develop trade, lift barriers, improved roads etc.. was because he wanted to emulate what Saito Dosan did to make his province wealthy without having access to the sea and nearly impregnable since he could attract so many brave warriors from around the region in his ranks.
Anyways, Saito clan playable would be a great addition to this mod really , also i am thinking that maybe it could be integrated with the new mod that made Imagawa, Mogami and Satake playable since we still have the traditional vanilla clans playable in this pack, so maybe it could be added by updating this pack and replacing the 'major' clans that are already playable in the main pack. Then maybe some minor clans as well for the gameplay value, like Nanbu to have something playable in the far north, Ryuzoji in the north of Kyushu and one of those clans in near Kyoto in the Chugoku region since Mori starts with a lot of provinces already in the far west of honshu and is the only playable clan in Chugoku.
One thing I do not understand though is why the start date was moved to 1562 instead of 1560 since Imagawa Yoshimoto was technically dead in 1560 at Okehazama but that is not a big problem though, just curious why it was moved forward since 1560 or even a bit before would be ideal as a start date, especially since we usually spend the first 20-30 turns getting techs and building an army but that is fine as it is anyways, not a big issue at all. This mod got me excited and playing Shogun again, hopefully you are still working on this mod!