Use your hands.
Yes, you heard that right. Use your hands for repairing pens. You're probably thinking "Well duh! Of course I use my hands". No, I mean use them more. What many of us don't realize is that out hands are the best tool in our repair-arsenal.
When I get a pen for work, and I going to remove the section or hood, I always try first with my hand. Think about it - Your hand is perfectly shaped for griping a pen. It has built in anti-slip material. It is sensitive, so you won't overdo anything, as you can feel what you're working with.
Your hand is perfect for tuning nibs too. I'd much rather align tines with my fingers than a pair of pliers.
The bottom line is this - (New repairers listen up!) You'll be tempted to use your tools all the time, because they're cool and fun. I often times used section pliers on pens that didn't need it, when I was first restoring. But all your doing is risking the pen more than necessary. Only use your tools when you really need them!
Your hands and fingers are your best tool. Don't forget it. :)