I can't answer all your questions, but I'll have a stab at a few.

Originally Posted by
taggalucci
Hi all,
I'm new here, so please be gentle!
Welcome aboard Tony!

Originally Posted by
taggalucci
I am considering a two shelf design with the lasers and optics on the lower shelf and the PSUs and scanner amps above. I will probably have a couple of fans on the upper shelf blowing into the unit with vents opposite.
Just make sure you have a positive case fan pressure, that should eliminate the build up of most dust.

Originally Posted by
taggalucci
I am toying with the idea of an airtight, dust free optical area. I have no idea how to go about this as I could not see much on the forum relating to this.
I assume everyone strives for this. Now I'm not talking hermetically sealed cases
But +ve case fans and an output window seem to work well.

Originally Posted by
taggalucci
I have a friend who's a sheet metal fabricator, so he's got access to various aluminium bits and pieces and can probably build the outer case.
Nice one. But don't get the aluminium done on the guillotine. (12-16mm is a bit ambitious for a guillotine anyway...). Invokes edge stresses and can lead to slight thermal warping. 12mm seems a really good choice IMO.

Originally Posted by
taggalucci
I have access to 16mm aluminium for the base plate, is this overkill? I also have access to 12mm plate.
Yes. I use 12mm on mine and that is loads. I can't think of any large benefit of the extra 4mm. Weight is a killer!
Some people use 6mm - but it warps and goes out of alignment if the plate temp increases.

Originally Posted by
taggalucci
Does anyone have any experience with creating sealed optical areas? I would be interested to hear about the pros and cons and what materials would be recommended to provide the seal and what constructions process people may have used for this.
Not me to that extent. See above...
One thing to remember: You WILL have to re-align at some point... every once in a while.

Originally Posted by
taggalucci
If a shutter was required for safety, as opposed to the alternative of killing power to the lasers, what sort of material should be considered a good beam block for 2W? What would be the most effective and inexpensive actuator for this shutter?
Black anodised aluminium? Not glued on though!

Originally Posted by
taggalucci
I plan to provide photos during design and construction.
Nice one! We like photos!

It sounds like you are going to have a REALLY nice setup there when all is said and done 
Quick question: Have you bought the 635nm yet? If not, you may want to consider 640nm setup for better beam spec.
Hope that helps,
Dan
- There is no such word as "can't" -
- 60% of the time it works every time -