first of all, wellcome and well done on deciding to make your own!!
you have most of the theory well established in your head allready, sothat makes suggestions easier 
1) given that you work with lower powers, a pair of safety goggles will block off all light at the given wavelength, so you will not see what you are doing. An alternative course of action is carefull planning, turning the laser power way down (an adjustable 0-5v power supply helps in this, to immitate a modulation signal) and either putting on a pair of sunglasses or two, or taking photos of the parts you are working on, to see what is actually happening. I find that using the flash also helps, as it reduces camera saturation. Safety goggles are a must at most cases, but during aligning they are not so usefull to me.
2) I would also ask around for a set of used DT25 ot DT30, instead of the PT20. I have PT40 and they are ok, I also have DT25 and they are too usefull (so usefull that maybe none will be willing to sell them). A good idea would also be to use a breakout board to wire everything ( http://shop.stanwaxlaser.co.uk/gener...oard-365-p.asp ) and have the iTrust card in its own seperate box.
3) Here are more possible dichro setups http://www.stanwax.plus.com/lw/dichro%20layouts.pdf In general, you want your strongest colour, possible the blue these days, passing through as many optics as possible, because there you have light to "waste". So a good order could be blue - green - red. And here is a helpfull guide in aligning http://www.stanwax.plus.com/lw/rgb%20alignment%20lw.pdf
4) Here it all dependes on how complicated you want to make it. At the moment, i would go for single mode diodes for red and blue. If you can't afford the expensive and sensitive opnext HL63133DG, you can try combining two of the single mode 110mw mitsuishi ones. The 638 nm wavelength is extra bright and you will not regret it a bit. i would actually advise against the 655 - 660 wavelengths. Sample and pricing here https://sites.google.com/site/dtrlpf...le-mode-diodes . the same gows for blue.. there is the normal 445nm "monster" spewing out more than a watt, and there is a 100mw single mode one, so again you have to use two ( https://sites.google.com/site/dtrlpf...m-pl450-diodes ). Ok, this is a more complicated route. You will need more optics, diode mounts, alignment but you will learn an awfull lot and you will make something that is more DIY. The great advantage using these diodes is very good quality beams that can fit on small galvo mirrors (so higher scan speed and less flicker)
5) Well, other alternatives are also available, cheaper too. But i will not even try to go against the pango tide here. it is pointless...
What i want to say as a closing remark, is that you don't have to make it all at once. You just need to calculate how much space you will require for all three colours and extra boards etc and sort out the baseplate and box. Then, you can go about adding one colour at a time
"its called character briggs..."