My only concern so far with your mods is the replacement of the window; that amber color is likely a filter for the wavelength of the laser, so that any spurious reflections while looking at the cutter work don't damage your eyes. Then again, that's just a guess (based only on using special safety glasses/goggles with a 200mW green laser pointer).
I might have to check ebay again - see how much the prices have come down since I last looked...Well, I just looked - and prices are down; really down since the last I looked. Your particular machine costs about $800.00 USD (+s/h); 40W laser tubes can be had for around $150.00 USD (+s/h). Much better pricing from when I last remember; of course, those prices are "drop-shipped from china" - and I don't quite trust dropping nearly a bill to a chinese supplier (I might be willing using escrow, though - did you use an escrow service?). I did find one guy selling from florida - but he only had local pickup (no shipping). Interesting, all the same - can't wait to hear how your mods and such turn out!
Re. window colour, everyone seems to make that comment
with an IR CO2 laser such as this it's the acrylic that stops the laser radiation, if it was a visible wavelength then it would most likely pass straight through the window but as it is, 6mm of clear is probably safer than 3mm of amber coloured dubious quality Chinese acrylic.
The amber colour reduces glare but I'm not stupid enough to stare at the burning material constantly
And going back to the clear window, look at universal or epilog laser cutters - you don't see any silly coloured window do you
Re. pricing, yes they have gone down a lot, I was rather surprised when I found I could get one so cheap. Mine was actually sent from the UK rather than direct from China, a lot of the sellers seem to have multiple places they ship from, look in the item description.
So lots more mods to come still, I think my honeycomb arrived yesterday as I have a suitable sized box waiting to be opened but unfortunately I was rather I'll yesterday so will probably spend most of today in bed :/