[Android Software Development] dafunk2:
All you can do is to exactly follow the OP. It's easy to make a mistake due to the hurry or not reading exactly. Anyway I will try to make some light:

1- Uninstall swype and reinstall it from Play store. Since you are on lollipop you can take the apk from the folder data/app/com.nuance.swype.dtc-1. Copy the folder including the subfolders ( lib/arm and the two *.so files) and paste it somewhere in your pc.

2- Take the "base.apk" from inside the folder in the point (1) and make a backup copy of this one (because you will need it afterwards). So now you have two copies of it. Let's say the Copy "A" and the Copy "B", perfectly identical.

Leave the Copy A as is and decompile the Copy B. Make your edits etc etc and then recompile it.

Now the Copy B is different from Copy A, right?

3- Take the Copy B just recompiled and copy it into a different folder , let's say a new folder called TEMP.

4- Rename the Copy B "base.apk" in "temp.apk.zip". PEASE NOTE: CHANGE THE FILE EXTENSION INTO ZIP!!!

5- Open the Copy B(.ZIP) with WinRar or 7zip (don't uncompress) and extract the files resources.arsc and all the edited *xml and/or *.png files into the folder TEMP. Close the WinRar window.

6- Now take the Copy A and rename it into "com.nuance.swype.dtc-1.apk.zip". NOTE: CHANGE THE EXTENSION INTO ZIP!!!

7- Open it with WinRar or 7zip(don't uncompress) and delete the file resources.arsc. Then drag into the Winrar window the file resources.arsc taken from the TEMP folder previously extracted. It will be added. Then drag and drop from TEMP folder each png or xml file in their respective folders into the WinRar window. Close the WinRar window.

8- Rename the Copy A (com.nuance.swype.dtc-1.apk.zip) into "com.nuance.swype.dtc-1.apk". NOTE: we removed the .zip extension so the file is back to the APK extension.

9- Copy the Copy A somewhere into the SDCard of your device

10- Now using your file manager copy the whole folder com.nuance.swype.dtc-1 (including the subfolders) from data/app to system/app. So you will have the structure like this: system/app/com.nuance.swype.dtc-1. Inside you will have a folder called "lib" and a file "base.apk".

11- Delete the file "base.apk" then copy the file Copy A (com.nuance.swype.dtc-1.apk) taken from your SDCard to system/app. Change the permissions for every folders and files, including the folder com.nuance.swype.dtc-1 and its subfolders (lib/arm) and the files *so. The folders need permissions 755 (rwxr-xr-x) and the files 644 (rw-r--r--).

12- Delete the folder data/app/com.nuance.swype.dtc-1. Reboot the device.

THAT'S ALL!

Feel free to ask, If I can be of any help.

Just a tip or two:

If you edit images with 9patch (with the extension *.9.png) be sure to drag into the file CopyA the recompiled ones. I mean that you will have to recompile the CopyB, then extract them from this one (because now are compiled) together with resources.arsc and the xml files. Pay attention to edit these images, if you're not sure how to do it make a search :)

If you edit some xml file from inside the foder res/values you will not find the same file or folder into the recompiled CopyB file. Don't worry, it's OK!! LOL

Good Luck ;)