There are probably a lot of posts with the same or similar issues , but I'll go ahead and post mine with as much info as I can.

-Issue : Game crashes while I am in the main house ( Cellar hasn't caused any problems yet)
-Addons : I have no addons this is a clean version of the game freshly installed from steam after I bought hearthfire. It includes Hearthfire , Dawnguard and the HD texture package.
-House layout : Greenhouse , Armory , Trophy Room , Cellar.
-NPCs affiliated with the house: Marcurio (As stewart) , Camilla Valerius (As wife) , Alesan and Runa Fair - Shield (As kids) , Rayya (As housecarl) and a Bard. Some times I see Faendal coming out of the main door.

First time I experienced crashes , was after I had most of the items in the house built. After brownsing the internet I found out that some people reccomended removing the workbenches would fix the crashes.
Well it seemed to work at first but as it turns up it didn't.
Anyway I went on and I adopted the two kids after a while first Alesan and then Runa. I found it strange that I could do that because I didn't build the extra bedrooms so at the moment we are 7 people in the house using two single beds and a double bed that are located at the second floor.

Now I will list the things that cause or may cause a crash.

- Walking into the house when everyone is inside. I think it has to do with the script that makes the kid run to me and initiate a dialog. I reached to that conclusion because whenever the kids were outside or asleep I could safely move to the Cellar and/or use the other items in the house (Greenhouse , satchel near alchemy table to store regeants , sacks near enchanting table to store Enchanted items to disenchant later and Soul Gems , bed)
- Using my wife's shop , started crashing my game as well (that didn't use to be a problem). My game would crash right after I finished trading with her.
- Trying to get lover's confort buff. Today I slept on the bed and I ended up with only well rested , I figured it had something to do with my wife being outside the house.
First try was using the bug (?) that Npcs follow you inside a door if they are still talking to you (Either from closing a dialog before their speech is complete , or the random things they say to you when you pass by them)
I slept right after and I got the LC buff , Game crashed after a while.
Second try was sleeping till night based on the fact that she has to come in the house eventually. Got the buff and game crashed when I tried to use a container in the house. (Didn't seem to matter which one cause I tried some of them.
- Reinstalling certain workbenches to finish the house decorations. I was still missing some mounted creatures decorations (the ones that show their hents on a wood thing on the walls) so when I got the materials needed for them, I tried installing them and after crashing a few times I quited trying.

Thats all the crashes I was able to connect with certain actions/situations.

Other bugs I noticed at the lakeview manor , that don't seem to cause a crash are the following:
-If you kill the hawks flying over the house , you get a body drop but they continue to fly over the house usually with an arrow or a couple of arrows on them. Shooting them again won't do nothing except of adding one more arrow on them.
-Iron veins near the cart won't respawn. I think it has something to do with Marcurio mining them from time to time but this doesn't seem to be the issue with veins inside mines (NPCs mining them won't deplet them)
-Mannequins some times move out of their position and some times they don't display the armor piece that covers their chest (Reloading either from save or re-entering the house seems to fix this)
-Chicken nest doesn't seem to respawn eggs. And having four chickens won't add extra nests.
-Apiary doesn't seem to respawn bees or honeycombs.
-Bee Hives and mushrooms (the ones that appear with adding decorations not mushrooms you plant) inside the greenhouse doesn't seem to respawn.
-Sprinting on the stairs outside the house makes you drop through them (I think I had the same issue with the ones inside the house).
-Random issues with the NPCs having issues with collision in and out the house , especially the kids.

Thats all I can remember atm.

I personally think that most of the crashes have something to do with the NPCs scripts because the cellar hasn't crashed even once yet , though I use it all the time. Alesan coming in there and trainning with his sword doesn't happen to often so I can't tell if it can cause a crash somehow.

The same rules for respawning items elsewhere applies to your house and its surroundings unless it has a separate respawning time like the garden, milk cupboard (if you have a kitchen) and greenhouse. Your iron ore, apiary, egg (chicken and occasionally the one on the roof) butter churn if you have the kitchen and any chickens killed will not respawn unless you are absent from the house for 10 days.

Makes no difference how many chickens you have, you only get one nest and one chicken egg each time the house resets, would have been nice to get a nest for each chicken.

Both the PS3 and Xbox 360 versions of the game had severe problems with autosaving after patch 1.7/1.6, any autosave would freeze the game for a lot of people, the PC version could have a similar problem. In Hearthfire a lot of people had trouble with crashing if they had the greenhouse at Lakeview Manor, some had trouble with the armory as well. And sometimes you can just have trouble with the house because of bugs while building, so rebuilding the house could solve it, or just going back and rebuilding different wings could solve the problem.

I don't think autosave is the issue for me ( Pc User) cause it doesn't happen anywhere else. You said something about rebuilding different wings. Is there an option for that ? Or you just use console commands.
I hope they release a patch fix soon enough.