This is the correct link (since he is a young account the URL is intentioanlly malformed by the forum)
First thing that I noticed is that you are short 5000 cargo space. It is best to have freighters with 5 Cargo holds (25000 cargo space) as that is the basic multiplier for factory sizes.
If you go to the construction/production screen for Earth and click on 'Stockpiles' do you see the PDC components listed in the relevant box?
It should be ship components in the top left, missiles in the top right, PDC components in the bottom left and then fighters in the bottom right.
*edit*
Use SM Mode to unlock and change your freighter design to be 5 holds, then go to the ship listing screen and cycle/click on each freighter so the existing ones are converted (using fairy dust) to the updated design. Then lock the design again and switch SM Mode off.
This means you wont have to redesign the ship from scratch and then retool a shipyard.