I think i will use rivets and "low module" sealant the same used in the glass facade industry (also used in the light carpentry, air conditioning and car conditioning/caravan industry).
I think spreading a thin layer of this sealant in between the "Ls" and allu sheets before riveting and then fill the gaps and the rivets ends to seal the inside of the boxes before glueing the padding inside (for this my choice fell on regular cheap camping/exercise mats) would do the job.
The only real problem are the corners, especially when the lid meets the rest of the case, a very easy solution is to make a sealed lid bigger than the body then fit a rubber seal to the upper edges of the case, a cars door protector is flexible enough and durable, so the water won't be able to "go up" and flood the panniers.

On the internet I saw some really beautiful cases but I never thought i was going to get those expensive "solution" from touratech :nono:, i used to make alluminium cases for myself a few years back (I have been a DJ with a very low budget start then for friends etc. - see some example below) and i know it is a job anybody can do with a low level of DIY experience.
I am willing to help anybody wanting to make their own cases as it is a very easy job and it can be done with a basic set of tools: drill, hammer, rivets, saw, screwdriver... that's it...
for the rack u may need some welding skills but not necessarily.
http://farm3.static.flickr.com/2144/...bdfdd3a998.jpg

http://farm3.static.flickr.com/2004/...8eddb1bdbc.jpg



I estimate 100 euro as the total cost but I am still working on them and will post some pics and more details in a few days.

Right click on mouse / click page info / click translate page into English

You will be better using a 'polyurethane' sealant/adhesive, silicone is acidic (which also attacks some metals) and not really designed for the rough and tumble of motorcycling/motoring:thumbup1: .
Stick (pun intended) to the Sikaflex or similar (Tiger seal eBay.co.uk - tiger seal, pu adhesive, Garage Equipment Tools, Motorcycle Parts Accessories items at low prices) product for long term waterproof/reliability,I have used this stuff, there is no substitute:nono:


Trophymick

I made my own top box and have the panniers cut and folded already. Need to weld them up and put all the fixings on it still though. I've intergrated a fuel or water tank in the bottom chamfered area of it. I didn't want square angles on the outside on areas that would hit the ground and leg side. But did want square angles on the inside. It's about 4 liters on each side. It will have a ball valve tap on the front back side of the pannier leaving enough clearance to the swing arm, and a filler neck from a boating shop on the inside of the pannier. Couldn't figure out a way to have it on the outside without compromising on the shape of the pannier.

Just didn't like the dimensions of the ones for sale. So I thought I would pack up my gear first and put everything in Eagle Creek pack cubes. Hate spending forever packing up everything all the time to keeping organised. Those cubes are the right dimensions to keep the total width within the handle bar widths which for me is the most important requirement.

This is the shape in cardboard and some CAD

http://i125.photobucket.com/albums/p...P2170256-2.jpg
http://i125.photobucket.com/albums/p...n/P2170257.jpg
http://i125.photobucket.com/albums/p.../3DPannier.jpg


This is the top box with electrical plug and hinged at the back on the DIY rack to keep access to the F650 seat latch.

http://i125.photobucket.com/albums/p...en/6240515.jpg
http://i125.photobucket.com/albums/p...n/P6240513.jpg
http://i125.photobucket.com/albums/p...n/P6240516.jpg
http://i125.photobucket.com/albums/p...n/P6240518.jpg
http://i125.photobucket.com/albums/p...n/P6240517.jpg
http://i125.photobucket.com/albums/p...n/P6240521.jpg

Trophymick,
my mistake in the description:
I will use a Butyl Rubber based sealant on the outside in between the bits before riveting and the low module silicone will fill the remaining gaps inside.

Tmotten,
I like the electrical plug, its a good idea. Just one thing: you cant remove the topbox from the bike?
Just an idea thrown in: there are sone take-apart (or slip-apart) hinges on the market they work as the normal ones with the added advantage that they can be taken apart letting you taking the lid completely off the case (the box from the rack in your case). If fitted instead of the normal ones u could still swing the topbox to access the saddle latch but also you could take the box off in a second.
Some pics below:

Take-apart hinges:

http://farm3.static.flickr.com/2366/...53a2b8e439.jpg
http://farm3.static.flickr.com/2121/...3499eef6ef.jpg

or Slip-apart hinges:

http://farm3.static.flickr.com/2034/...4653c415_m.jpg

Get Alpos boxes - half the usual price.

OH NO not another giant top box on a big trailie!!!:censored:

Very nice boxes indeed especially the F Series but do they make something the size we need? 782x585x412 mm seem too wide IMO.

link here by the way: Alpos - F Series

Not to worry. It's only for big overland trips. In Aussie on weekends or longer I ride like this. No camping though but I'd probably go for a strap on tent and sleeping bag arrangement.

http://i125.photobucket.com/albums/p...n/P6100424.jpg

I'm not too worried about the size if the weight is kept down. Last time we rode accross northern Asia on a Tenere that Dave Lambeth setup with 2 x 6 litre Acerbis tanks on the back. He really liked the setup so we thought we'd go with it. It was pretty successfull, but that weight would be more than we will be putting in those boxes. That's why I like building boxes around the luggage rather than the other way around. On trips like that it's all about the getting there eventually in any way shape or form, so you tend to take it easy.

I would have to remove the 6 nylock nuts, but that is the idea as I would only use this on long trips I reckon.

I have had a quick look at those hinges, but wouldn't I need to build a brace or something to stop them sliding off?

Take-apart hinges
 

Only the Slip-apart ones may need something that stops them from sliding off sideways but i noticed your mechanism to secure the topbox to the rack, that woudl be enough.

The Take-apart ones dont slide sideways, in order to take the lid off u need to open it at least 90degrees.
Here is a better picture:

Has anyone actually made wood panniers? - just curious about:-

What detail was used to fasten them to the bike.
How they are performing.
If there is a "cutting list" for whatever size was made.

Marine ply is water resistant because of the glues used in manufacturing it and WBP (water and boil proof) glue might be appropriate for the joints. Modern glues for timber are stronger than the timber itself. Nevertheless, a painted, or other similar varnish, finish would help to shed water.

IMHO it is very important to minimise any potential injury to yourself by rounding off corners and avoiding sharp edges and brackets .
In case of an accident I would not want to get my leg stuck under the sharp edge of a pannier or be whacked in the back by a large hard top box .

Panniers should be strong enough to support the bike if it falls off the stand or in a slow speed tumble .You will only get that kind of strength by welding and maybe double skinning the bottom and sloping sides [ refer to tmotten" design ] , or by adding a steel frame underneath [ Grant's design ] .
Wooden panniers would be fine with a steel frame around them to give added support in case of an accident [also the condensation would be much less in a wooden case] .

Made the racks and welded brackets to the ammo boxes and they work great,ammo boxes 10 kg,alloy boxes 7.5 kg each,I might not bother to upgrade to the alloy ones.

Nice. Where did you find them?

the picture here:
Hardware - PlanetDJ.com

also a nice selection of hinges here:
Penn Elcom - Flight Case and Speaker Cabinet Solutions

u can find this tipe of accessories where they make flightcases or custom alluminium cases, they are nothing special really, i used to buy them from a shop where they also repair luggage and trunks.
U can also try a big hardware shop.

After a little Google search it looks like marine suppliers keep these kind of things. Try to Google this: "take apart" hinges.