all of the Custom fields won't show up

Hi,

1. Only the fields with a value selected/entered will display in the specification area of each product. If you leave the field empty, it won't display the row for the product specifications.
So it's normal as far as I can see.

2. You can edit the file "compare" via the menu Display>Views and add your text just after:
<span id="hikashop_product_<?php echo $element->product_id; ?>_price_main" class="hikashop_product_price_main">

3. Sure. Instead of entering the quantity of all the variants of the product in the "quantity" field of the main product, click on the "manage variants" button of the product and edit each variant of the product to enter the quantity of the variant.

4. I'm not following you. Could you give a link to a product page with the problem so that we can see that ?