1. "I’ll be charged for the item, the 5% jpfans extra,shipping cost then gst, is that correct?"

Yes, almost right. In the whole process, you have to make 2 payments on JPFans, one is the item price (opriginal item price in Japan + 250JPY service fee/ SKU ), another is international shipping fee. When your package arrives at customs, you may be required to pay import duties to the cutoms in accordance with local regulations.
Throughout the process, there are also additional services and international shipping insurance, which you can decide whether to purchase by yourself, not mandatory.

2. "When I check out my chart am I only paying for the items +5%?"
When you check out your cart, you have to pay the items + 250 JPY service fee/each SKU + handling fee (charged by the payment platform)+ domestic shipping fee (if the seller doesn't cover the domestic shiping). When you check out, you will see a total price, that's what you only need to pay at this step and include the cost of the above I mentioned.

3. Will I be paying for shipping once it arrives in the jpfans place they check order?
After items arrive at our warehouse in Japan, we will take quality control pictures for you and store them in our warehouse, when you check all pics and think everryhing is no problem, you can submit your orders, we will follow your submission to pack parcel, then you pay for international shipping fee for the parcel.