1. Both JB3 and Improved Atmosphere are NOTORIOUS for causing crashes, bugging, and exacerbating the inherent performance issues.
2. You don't indicate whether you've patched the game with 4GB or LAA.

Suggestion:

1. Patch the game with 4GB/LAA.
2. Remove all mods and run the game as far as completing character creation and entering the initial area, to confirm that things work properly in that state. (Use a throwaway character for the unmodded pass.)
3. Once you've confirmed the vanilla game works, reinstall all your mods (making sure to also install any additional requirements) apart from IA and JB3.
4. Run the game again with a throwaway character, again as far as entering the first map.
5. Once you've confirmed that the game works with those mods, add back either JB3 or IA, if you really can't live without them. Repeat the throwaway character process again.
6. Keep adding back mods until you know that the game works.

Additional suggestions:

1. Turn off any in-game overlays, like the Steam or Origin overlay.
2. Use a Windows compatibility setting for the game, like Windows XP SP3.