Mike,
From a beginners point of view, lets have a go at answering your questions,
1. Because of the bulid up of biofilm in smaller diameter pipes, I would use nothing less than 25mm (1") diameter and with the size of your systems fish tank (pond at approx 33000 Litres) I would be using 50mm (2") for the gravity feed to your grow beds. If you are relying on Gravity feed to your Grow Beds, in Parallel as you intend, then they must all be at the same level for the inflow to balance the feed to them at the same rate. I personally don't think it is a good idea to have GB's in series because of the different take up of nutrients as the water flows from one to the next, to the next, etc.. Even so, I would put a serviceable ball valve to control the flow to each GB for fine adjustment.
2. The two best choices for through liner fittings are "bulkhead" or "tank" fittings:
http://www.aquaponics.net.au/product/prod20.htm Threaded connections with compression washers and Nut, or a "Uniseal": Push through grommet with lip seals. Both readily available. Just putting a pipe through the hole/s and sealing with silicon doesn't really provide a long lasting or certain seal. Both Uniseals and Tank fittings are available in sizes from 19mm to 100mm.
3. You don't really need to put gravel in the bottom of your fish pond, unless for aesthetic reasons, because bacteria will develop, start to convert your dissolved and solids nutrients, take away those nutients from your Grow Beds, bulid up anaerobic spots in the fish tank, without regular cleaning, with that solids conversion and end up perhaps producing toxic end products that your fish don't need. Let the biofilter take care of the solids deletion and the other 75% of dissloved nutrients go to their best effect in your Grow Beds. So I would recommend not putting Gravel in your Fish Pond.
4. If you want your 24/7 Biofilter to be effective in ridding the pond of solids, then the lower down the suction inlet to the bottom of the pond, the better. Unless you are relying on the fish to stir up the bottom so that the pump can draw in "the floating" matter, I would be putting the pump on the bottom of the pond and if it meant regular cleaning to rid it of build-up then so be it. Although you could put a fine sceen, self cleaning surround filter to the pump inlet, but this would also require regular maintenance as well. This is also a good reason not to have gravel on the bottom of the pond, let the fish stir up some sediment without the availability of it being 'trapped' in a gravel bed.
A couple of other points.
If you use auto siphons in your Grow beds for the Flood and Drain cycles, you don't need an electronic or other timer on your Sump Pump. Just one less thing to break down or go wrong IMHO.
I would use a "Tee" pipe wier at the outlet from your pond and not just a piece of open pipe, and possibly from a purpose made sump in the bottom of your Fish tank/Pond, to take water from the bottom of the pond rather than just from the surface. This will better ensure that you are moving any solids into the GB's for breakdown etc. This will also stop any of your fish (and any other curious critter) from deciding to explore the surface opening in your transfer pipe to the GB with obvious deadly results!! For the fish anyway!
Anyway, that's my opinion, and I normally get someone saying I'm completely wrong, but I'm used to that by now. Please post a couple of pics to show your progress and in-situ operational parameters. I'm sure you will get good, reliable advice on the future sucessful operation of your system.
Cheers IanK
Backyard Aquaponics
