I'm literally on a flight from NYC to SFO right now and was putting together an evaluation of this 15 minutes ago because I'm trying to weigh the benefits of using Amazon for fulfillment.
FBA seems to have a variety of charges as you'd mentioned and here's a breakdown of what I found:
Monthly Subscription: $39.99/month
Referral Fee: 8-15% (This depends on what type of product you're selling Consumer electronics are 8% for example and it's a minimum of $1.00/item)
Pick & Pack: This depends on size/weight
Weight charge: This depends on weight
Shipping: This depends on weight)
Storage: This is charges per cubic foot and fluctuates on the time of year
This also doesn't take into consideration the costs of getting your product to Amazon's warehouse in the first place in addition to manufacturing, etc.
Self Fulfillment has a referral fee (depends on category of product,) per item fee ($.99/item) and you still need to account for your own packing/shipping. You also need to consider the time it takes one of your employees to support this.
Hope this helps,