Lemme share my recent total loss experience.
I had a difficult to find (in the secondary market) 1999 Ford Crown Vic LX with the Handling and Performance Package.
To keep it simple, the insurance company devalued all the extras on the car to zero due to age and gave me market value on a standard Vic.
I also had aftermarket items on the car such as:
Alarm
Cd Changer
Mud flaps
window tint
etc.
Have all receipts and they devauled these by 80-100% of original price.
I got hosed.
You will too, so mod away, but know that if you expereince a total loss, you will not be fully, if at all, covered for mod items.
There is agreed value insurance available. It's expensive and varies greatly depending upon how often you drive it. If it's a parade car, it's affordable, but for daily drivers it's probably not very attractive.