Only reason I am writing this is many have come to me with issues they encountered. Plus the many tutorials i've seen have just been copied over and over. Hopefully if you do decide to install cydia manually this will help.
WARNING: If you have a password set or touch ID, do not do this you will get stuck in a boot loop and will have to restore.
Read Why
Note: PanGu v1.0.1 seems to make iMessage not work correctly.
The Tutorial.
First download cydia-lproj_1.1.12_iphoneos-arm.deb, then download cydia_1.1.13_iphoneos-arm.deb. Both files can be found here. Debs by Saurik
Make a folder on your desktop named Cydia, inside that folder make one named AutoInstall. Now take the two downloaded files, and put them in the AutoInstall folder.
Using this tutorial open cyberduck, and login to your phone.
http://junesiphone.com/tutorials/cyberduck.html
Something not in the tutorial above is how to find your phone's ip address. To find it go to settings, click wifi and tap the i. It will show your ip address.
When logged into your phone navigate to /var/root/Media/ drag the Cydia folder you made to this location. Now open it, then open the AutoInstall folder. You should see the two debs you put in there.
Right click cydia-lproj_1.1.12_iphoneos-arm.deb and select info. Click the permissions tab and type in 777 press enter. All boxes should be checked. Do the same for cydia_1.1.13_iphoneos-arm.deb
Reboot your phone and you will have cydia installed.
I do not have a windows PC, but this same thing can be achieved with WinSCP.
If you have any issues my Twitter is @JunesiPhone
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