*Attention*: A partial fix for a lot of the issues in this bug list plopped in my lap by accident this morning.

Run the launcher, set graphics to ULTRA, then go to advanced and manually alter settings as you find you need to (shadows/et al).

The biggest concern is that you should leave HDR on if at all possible, turn Vsync OFF unless the new settings cause visual tearing, and set Water Multisampling to LOW.

Adjust your other visual sliders as needed, but a good rule of thumb for running fallout 3 was to set them all to HALF of their max, or 1 'tick' above half, with the exception of tree LOD which should be at about 75% of max, and land quality which should be at max at all times (150%).

Problems this solved:

1. Body parts appearing in first person, obscuring view. Selecting ULTRA fixes this..no idea why.
2. Arms and weapons moving around oddly while moving (especially crouching). Selecting ULTRA fixes this..no idea why.
3. Weapons and weapon arm (where applicable) vanishing at random, only reappearing during iron sights (and sometimes not even then). Selecting ULTRA fixes this..no idea why.
4. numerous stutters and freezes.
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Fixes 2: WRYE FLASH!

1. Download and install Wrye Flash and the proper python version.
2. copy and paste the launcher .pyw file onto your desktop for fast launching of Wrye.
3. Run the masterupdate setup .bat file.
4. close the program.
5. Open FOMM and click on HELP, then on CHECK FOR UPDATE. This will check for an updated BOSS load order schematic.
6. Update the load order in FOMM.
7. Close FOMM and re-open WRYE
8. To double check load order, hit the BOSS button in Wrye. If anything changes, hunt down the masterupdate.txt file for FOMM and open it and manually check load order vs the list in that file. THIS SHOULDN'T HAPPEN.
9. Make sure BASHEDPATCH,0.esp is at the very bottom. always. no matter WHERE BOSS put it..always relocate it to the very bottom!
9a. (NOTE: You can move an item up or down the list by clicking on it and holding down ALT while pushing the UP or DOWN arrow keys)

10. Now highlight every file in the list, including the bashed patch, right click somewhere in the list and select MARK MERGEABLE
11. Once its done doing it's thing, click on bashed Patch, 0.esp so its the only thing highlighted. Right click and select REBUILD PATCH.

Most of the options inside are not needed, except :

Alias Mod Names
Merge Patches
FormID Lists
Leveled Lists

Click on BUILD PATCH and wait for it to finish. Observe any pop ups asking to uncheck files that will be merged, et al, and wait for the results box to pop up.
When its done, any files that it wanted to 'merge' should now be in the list with a + in its check box instead of a check mark.

Barring any unforseen problems...you are now DONE and ready to roll.

WHAT THIS FIXES: *most* Random crashes and lockups. Helps reduce game slowdown. Is not 100% panacea, but avoids tons of conflicts that can crash your game or ruin a save file.

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FURTHER ADVICE:
1. Turn your blasted RADIO *OFF* before saving. The sound system is hinky and can lock up on loading an active radio. Radio can also lock the system up during a save.

2. Never save while 'autorun' is on (default 'Q' key). This can cause many issues, your untimely fall from a great height not the least of them.

3. USE THE CONSOLE: default in America is the tilde key ( ` ) . In the console type SAVE "enter a name or description" (include those quote marks!!!)

Good luck, and good gaming.