Hello,
I'm having bloat related problems since 1.5 patch. I hoped that 1.6 beta (1.6.87) and 1.6 (1.6.89) will fix the game, but they made it worse! I'm using some mods (10 small ones), but I isolated the problem and it comes solely from the patch. Here're the facts:
Before 1.5 - save game size - 15mb (180 hours game time), game is fine and smooth.
1.6.87 beta - save game size - 18mb lags and freezes every 1-2minutes for 2-3 seconds (no fps drop)
updated to 1.6.89 and after 20 minutes the save size went up to 22mb (freezes for 5 seconds, occasional ctds). I uninstalled all mods, dismissed follower, went to my house, slept for a whole month and the save went up to 23,500mb
Manually reverted back to 1.6.87, played exactly 1 minute and the save went from 23mb to 22mb with all mods activated.
So the problem clearly is the patch!

I developed a bloating paranoia. I want to enjoy this frikin game, not to watch every 10 minutes my save game size, to be careful not to move objects. I reverted back and replayed so many save games, every lag or freeze freaks me out! I want to play a game, not to learn its mechanics and programming to able to avoid bugs!

Please Bethesda, fix your damn game! EVERY SINGLE patch is making this game buggier and more unstable!
And please, don't start asking if I reinstalled the game, what my computer specs are and if I reinstalled my windows!

A few things:

1) Please post your load order. Your mods may not like the new patch, the size of your load order is irrelevant, and your mods may need an update to work properly with 1.6 (Especially those that rely on records in the Update.esm).
2) Some save fluctuation is normal, especially on older saves where it has more to keep track of, and most especially when you have mods (Certain mods casue more fluxuation than others). Bloat is 99% mod related.
3) Bloat is not going to magically go away when you uninstall mods and do a save. The cell reset will not clear out any bloat related to scripts, it sounds to me like one of your mods has an errant script that worked ok under 1.5 but does not like 1.6. The script may be "baked" into your save.


As for your performance issues:
1) You need to make sure that after updating to a new patch (or reverting to an old one), or updating any drivers, that you delete your Skyrim and SkyrimPrefs inis in your save directory, and then open the Skyrim launcher to generate new ones. Do not change any settings yet and try playing the game with the detected settings 1st.

2) I've noticed that for some people, their issues (mainly graphical) were solved after updating their drivers.

3) I will ask for your computer specifications. There have been plenty of issues on the forums that the community could solve with PC specs and a good ole DXdiag, and is just plain ignorant to think that this is irrelevant.

4) A reinstall of windows is really over-the-top and should be an absolute last resort when troubleshooting, and a re-install of Skyrim is a 2nd to last resort. A new installation of windows would eliminate anything that could possibly be interfearing with your game, and has helped in past (Again, stricktly last resort, I wouldn't advise that in this case personally).

5) Try doing a clean boot, or at the very least, disable any anti-virus you have running in the background when playing Skyrim. This has caused both CTDs AND hitches/stuttering for me.

Edit: Just thought I'd clarify on something. Regenerating new inis when a game is updated, is reverted to an old patch, or when you do driver updates is necessary (In my opinion). Bethesda did make performance optimizations in this patch, new inis would ensure that these changes are properly implimented (For example: Grass shadows can now be turned off in the ini). This is more important when updating drivers as your system configuration has changed.

I disabled all mods in order to see if the bloat will go away. I slept 30 days, waiting the cells to reset. The bloat increases without mods. If I start a new game or revert back to much older save (save game size below 18mb), the lag is gone. So its clearly a save game related problem.
And computer specs and reinstalling windows was a ironical joke, because I played this game since the launch with the same computer and the same drivers and it was fine. After the update I installed the new nvidia video drivers, I noticed a fps boost, but the lag is still there. And its easy to tell that the lag comes from bugged script in the save game, not my laptop performance or antivirus software. Hell, I played Skyrim on diagnostic start up.
But as you wanted here's my mod order:
Mod Load Order Index
Skyrim.esm 00 1
Update 01 2
Claralux 02 3 - adds lanterns to the cities
Unofficial Skyrim patch 03 4
Cloaks 04 5
LFarmors 05 6
BDO 06 7 follower dialogue overhaul
possesivecorpses 07 8 de-bloating tool
better villages 08 9
dovakhin can relax 09 10
multiple followers 0A 11
spouse custom home 0B 12
RwAzura 0C 13 custom player house
Valkyrie 0D 14 new npc
HousecarlWhiterun 0E 15 new looks for Lydia
Eola 0F 16 new looks for Eola
sorry, I can't post links.

And my specs are: laptop Dell Inspiron 1520n, Intel core duo 1,5ghz, 4gb ram, Nvidia 8600gs 128mb. I know its a very slow laptop, below the minimum requirements, but with tweaks (low res textures) I can play smoothly (40fps) on low on 800x600. (I love this game that much to be able to stand this low resolutions)