To start with mods or not to start with mods?

Basically, my problem is that when I install the mods, I create a new save (As I just installed the game, and found the mods) but as soon as I go into the game, my 'compliment' is practically just a mess of a character, and near the end where you have to shoot a helicopter, it spawns under the building. I was wondering if I had to do a few missions first without mods, and then install the mods. I remember on the SR2 Mods it was recommended to install them before creating a new save. Any ideas?
 
Some of the new taunts/compliments in the mod by turk or shitface have broken rigs, and only exist as something amusing. Simply going to the plastic surgeon will let you change them and choose what you want (including the originals.)

The heli issue means you installed the mod to change all helicopters to boats so you can customize them. That mod was intended to be removed after you customized them. Otherwise, the helicopters act like boats and fall to the ground from the sky in missions. You'll want to only to temporarily use it after getting to the open world.
 
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