There are two parts to your question

1. **Factory Reset**.  

a) Factory reset removes user data including apps installed by the user on phone. Since your device is rooted, you can see that everything in  `/data`
and `/data/data` will be wiped.

b) Factory reset does **not** flash stock ROM. Since you have deleted preloaded apps, they will **not** be restored. If you want them restored, you have to flash stock ROM

To understand more about factory reset, please read this

http://android.stackexchange.com/questions/12802/factory-reset-to-restore-performance-what-are-the-disadvantages

2. **Root**.  You will **not** lose root on factory reset. Your phone will remain rooted

Please read this post to understand more http://android.stackexchange.com/questions/100996/can-i-safely-do-a-factory-reset-without-losing-root