Downtown Boston (Faneuil Hall, Haymarket Mall, Goodneighbor, Old Union Church, Shenley’s Oyster Bar) is extremely dense with multiple spawn markers, events, load doors, and containers all packed into a small area across multiple cells. If you’re having problems there, it’s more than likely a result of having too many mods doing too many things.
If you've never been able to get there without mods, you are not going to be able to get there with mods.
Leveled Item Lists
Game engine limit
Downtown is rife with spawn points that, when overloaded with high-poly weapons or armor mods, will cause problems. Just as the amount of plugins the game can load is 255 (on PC), the amount of forms in the level lists for all BGS games using the same engine is 255. Once a level list has hit this limit, it effectively breaks the game.
Poorly implemented lists
Unfortunately most mods that use A_Blind_Mans free resource script -- which is a common script to use instead of requiring the DLC which has optimized code in it -- have script injected weapons into the wrong lists. Additionally, the script itself may or may not optimized, depending on the version used. Nested arrays with undeclared lengths take longer to cycle through.
There is no way to know on console if the script injection will add to the process time of entering a cell, and there is no way to know if those weapons have been injected into the correct level lists. Always make a test character and go to several spawn points with Gunners, Raiders, and enemies with pistols and shotguns -- those seem the lists that have the most errors.
ModCols, which are specialized level lists for weapon mods (like barrels, etc), armor mods (like linings), and robot mods (like robot armors), can only be modded once per load order, and there is no way to script-inject them. Using multiple game modifications for the same weapon, armor, or robot piece must be patched in order to use together. It is best to choose only one mod to modify ModCols, otherwise players will be maintaining a list of only patches. The in-game mod menu on console does not recognize ESLs as any different than normal plug-ins and all ESLs regardless of ESL flagging count against console slot limits.
Overbuilding a Settlement
The game has built-in limitations for a reason. Downtown -- in particular Faneuil Hall and Haymarket Mall -- is extremely sensitive to having overbuilt settlements. It is recommended to only build up one settlement per play through if you're going to be using Fallout 4 as a building sim, and if you are questing, do not begin building until most of the quests you want to build are complete.
Precombined Data and Optimization Systems
When precombines are disabled, Downtown Boston is among the first places to show a noticeable performance hit. There are tweak mods that are designed with the intent of making the area better, but actually make it worse on accident, so be sure to double check prior to downloading.