Comskip Issues and Audio Out Of Sync

Hello All,
I’m new to Mcebuddy and bought the premium version. Please be bear with me.

Question 1:

I am having an issue after trimming the first few seconds of some of my videos the audio becomes out of sync. I do not have an audio delay checked off. What do I do?

Question 2:

Comskip doesn’t seem to remove all of the commercials especially towards the tail end of the video in between the credits and the end of the program. How do I fix this?

Question 3:

How do you change the seconds in the transition between the cut commercial and the video?

Question 4

How do you customize the Comskip to remove commercials it’s missing?