SMS function mod is available in some custom ROMs, for stock ROM mod please refer this.

If you only rooted your device then probably it is fine to install the OTA update without any issue. The system files that I refer here are those files in /system, /sys etc.

Asus MY, check first page for the location.

Corrected, thank you

Did you use factory image or you sideload the OTA zip file?

If you use factory image then it will unroot your tablet automatically, no need to do extra steps to unroot it, if you are going for warranty purpose, then you need to relock the bootloader after flashing factory image.

It happens to me sometimes when the device is connected to PC for a long time, just need to unplug it and plug in again.

There is a native battery percentage in 4.4 which can be activated by adb shell command but it will only show you when it is below certain level due to the color similarity with the icon. Info here

Most of the third party app can be installed to show the percentage but since you don't want to install third party app so the choices left are the method posted above or use a custom ROM. Xposed Framework can do this too but it is considered a third party app, it's totally up to you whether to use or not.

For home screen button issue, it is 4.4 software issue now and is affecting most of the Nexus 4 users according to the Google bug tracker site, so probably affecting Nexus 7 too.

You need an app called YAMTT and place your tablet on a flat surface, put your finger on the top and bottom of the screen and slowly move to center, if got touchscreen issue, you will see ghost touch on the screen.

Yes, go to Hotspot LYP, they are selling at RRP if I am not mistaken.

Price not sure but you can always ask them here.

Try force to LTE only, dial *#*#4636#*#*, select phone information, choose LTE only and see if your network status shows 4G/LTE(depending on your ROM) or not.

There are few ways:
1. Some custom ROMs have dialer option
2. Install ICS Dialer
3. Settings > Connections (tab) > More Networks > Mobile Networks > Network Mode > Change the network mode between LTE/WCDMA/GSM (for LTE) and WCDMA/GSM (for non-LTE)

PSX not bad

Should be the cheapest in town.

Maybe your OTG cable is faulty?

Go to Google Play Store app and verify is your download still running, because the downloading status will only show up in notification tray if you have active download session on going. So far I don't have this problem on stock ROM, haven't tried other custom ROMs yet as not all features are ready for daily driver yet.

You using Trickster Mod app? If yes then you don't have to worry about the min frequency, once you set it to a certain value, i.e. 384MHz, it will stick to it, just some display error in the app still showing you the default frequency, i.e. 1026MHz. Make sure you have enabled the "Set on boot" so everytime you reboot your tablet, the value is set automatically.

Are you running stock ROM?

No idea then, I don't have this issue on stock ROM. Maybe try a reflash?

Thread updated with Android 4.4.1(KOT49E) OTA zip file, currently only for LTE model(deb), WiFi model(flo) OTA zip file link will be added once it becomes available on the Internet.

Download link in first page.

Yes, download the supersu.zip from Chainfire website and flash it in custom recovery. No toolkit is required.

Got, captured LTE model OTA link so far, waiting for WiFi model OTA link to sideload it.

OTA rollout is done batch by batch, for example, first batch only 10% of the devices will receive the OTA update, second batch 25% and so forth so Google can stop the rollout when serious bugs are found in the OTA and fix it before all devices are affected by the bugs which can cause serious issue for a large users base OS.

First page added with WiFi model(flo) 4.4.1 OTA zip file download link.