So I had a Moto E that was showing weird issues. Sometimes when it’s rebooted it stucks in bootloop and fails to finish the boot sequence. The home screen just doesn’t appear. I manage to flash a fresh ROM on it and after which it starts to work. I haven’t been able to identify the problem yet, but the turnaround is working good as of now. So I just want to document the process of fixing the soft bricked Moto E:

*** DISCLAIMER ***
Please note that this is just a documentation of the process I followed to fix my Moto E. This is by no means an accurate or official guide to fix your Moto E. If you do mess up your phone trying to follow this documentation, you can't blame me.

The simple procedure for a fresh Moto E is to first unlock the bootloader of Moto E. Which is a simple one time process which includes using the following command in fastboot mode: fastboot oem get_unlock_data. The unlock is complete when you enter a code on Motorola website and they give you a return string to unlock it. The guide is here.
Once the phone is unlocked its time to flash a custom recovery. This is done by downloading the TWRP recovery for Moto E here:  http://d-h.st/1Zp.
And then booting the phone in fastboot mode and sending following command:

fastboot flash recovery moto_e_twrp2.7.0.0_v1.2.img

Once the recovery is flashed you can reboot in recovery mode manually or by following command:

fastboot reboot

From recovery mode you can do all sorts of things like clearing out the cache (which sometimes fixes issues), and going into adb sideload mode. From this sideload mode, you can send sideload commands which can be used to install a custom ROM. The custom ROM for Moto E can be downloaded from below link: http://forum.xda-developers.com/moto-e/development/rom-stock-motorola-lollipop-rom-t3167111. (The one which worked for me was: Retail Dual-SIM (Asia | World) 5.1 ROM (Optimized) v1.1 (287mb) Deodexed).
This ROM can be sideloaded by going into the sideload mode and sending following command:

adb sideload "I:\Moto E\XT1022_Retail_DualSim_51_Optimized_v1.1.zip"

After the above command, it will take some time and progress can be viewed on phone. Once that’s done you can reboot the device and the phone should start. First run takes a lot of times since it “optimizes” the app etc.
This ends the procedure. If you want to recreate all partitions from scratch, you may try to follow the following guide of flashing the stock firmware: http://forum.xda-developers.com/showthread.php?t=2759495.
The above guide tells to download the stock firmware from following location:

http://forum.xda-developers.com/showthread.php?t=2755857

(I choose XT1022_CONDOR_RETAILDSDS_5.1_LPCS23.13-34.8-3_cid7 (Newer Build))
To flash the stock firmware the above guide says to follow the below series of commands:

fastboot flash partition gpt.bin
fastboot flash motoboot motoboot.img
fastboot flash logo logo.bin
fastboot flash boot boot.img
fastboot flash recovery recovery.img
fastboot.exe flash system system.img_sparsechunk.0
fastboot.exe flash system system.img_sparsechunk.1
fastboot.exe flash system system.img_sparsechunk.2
fastboot.exe flash system system.img_sparsechunk.3
fastboot flash modem NON-HLOS.bin
fastboot erase modemst1
fastboot erase modemst2
fastboot flash fsg fsg.mbn
fastboot erase cache
fastboot erase userdata
fastboot reboot

I had to still try to flash the custom ROM instead of stock firmware to get my Moto E to successfully boot.