How to find the root of android slow down I have samsung galaxy nexus with CM-11 nightly 07-04-2014.

About twice a month I update my version to the latest nightly build and it was pretty good for a while. Unfortunately last time ( for a couple of weeks ) there were two updates which really slowed down my device. Every app starts now up to 10 seconds. Even when I get a phone call sometimes the phone is not fast enough to display me an answer call button. And the network became slow as hell. CM update download over wifi will take up to several hours, while before it was about 5 minutes. However wifi in local network works a bit faster. gprs inet also works very slow. 100K pdf download takes up to 5 minutes, while it was up to 10 seconds before.

I tried to downgrade to the last stable version I had ( it looks like any before 03-25 ), but without success. 
Important note: I did not perform the whole wipe during downgrade. I only formatted /system and /cache. I also tried to install other nightly builds with the same result.

There is nothing suspicious in dmesg or logcat. Sometimes in dmesg I can see messages about killing some users apps but it seems normal to me.

How to find the root of such slowdown?

And I'm not sure if the whole wipe will help me, as I'd like to save app data and restore it after wipe.
As far as I now Android device slowdown can occur for several reasons:


Very low amount of free RAM.
Check under Settings>Apps>Running how much free RAM you have
If your free RAM is too low (70-150MB or less) it's probably the cause so check which app/apps, if it's not an app maybe it's a bug in the ROM. (see 3)
Low free space on internal storage. (check under Setting>Storage)
If the free space is too low (~2GB or less), try free up some space and check if that helps
Kernel bug/misconfiguration.
Try to check your CPU usage stats, clock speed, governor, number of active cores etc...
(If you havn't flashed a custom kernel and never changed the governor/clock speed or other performance settings it's probably not the problem)
ROM bug
You can try perform a nandroid backup, then reinstall the rom after full wipe and see how it performs, if it's still slow, try clean install of the version that previously worked fine (only if you know what you doing!)
Bug in one of the user apps.
If your CPU/RAM usage is too high for no reason maybe one of your apps eating it.
I recommend you to try OSMonitor or any similar app to find which app eating your CPU/RAM.
(Lack of TRIM, TRIM does exist in Android 4.3 and up so it's not the problem)
(In some rare cases bad sdcard can cause such problem but it's not the problem too since Galaxy Nexus doesn't have card slot)