Skyrim mods interact strangely at the best of times. I know a modder who was working on something to do with Fort Dawnguard, and his edits ended up affecting things in Whiterun and Falkreath. How?
It also may not be mod related. Are you using the alpha build 1.7 for SKSE? If not, you may need to investigate how to allocate more V-RAM to Skyrim, as the update for Skyrim 1.9 basically borked how memory is allocated towards the game. If it exceeds a certain limit....you crash to desktop. 1.7 has this functionality built in, so it's not a problem.
BOSS and LOOT are programs which, when run, will tell you what order to put your mods in, what dependencies those mods have (and if they are present or not) and whether those mods have "dirty edits" which require cleaning. TES5Edit is a program which allows you to clean the mods. Neither BOSS or LOOT is perfect, but they are frequently very helpful.
Also, I echo your feelings about Hunterborn. It is a great mod. It's even better when combined with RND and Frostfall, and either played with the SkyRe overhaul (which has a new perk tree - Wayfarer - which deals with survivalism and is awesome) or with Requiem, as the mod author recommends.
The only problem with Hunterborn is that it's not entirely compatible with some other major hunting overhaul mods. Notably, it has problems with SkyTEST when it comes to looting...as I recall, it's not a CTD level problem, but more to do with the kind of loot you get. That info is contained in the compatability information though (the author is very
good at that), so it's easy enough to find. The other problem is that it can be, at times, rather script intensive, which can slow down your system. This is a notable issue when it is combined with Frostfall.
Hmmm, now I think about it...does ACE Archery, Melee and Realistic Fighting play nice with Hunterborn? Probably not, I've not seen anything about a compatability patch or anything. Even if you're not using Scrimshaw arrows and weapons, they may not be recognised by the ACE system, and so could be fouling things up. Just a possibility, but one to keep in mind. If that is the case, I suggest perhaps using SkyRe as a combat overhaul - it's just as valid, and probably a little more coherent overall, and you know for sure that it has SkyRe compatability.