An excellent book, one that I can't recommend highly enough.
A friend at Caltech took this a step further and came up with his own crude SoC that took input from basic switches, did calculations based on code taken from a small off the shelf EEPROM, and displayed the output to segment LEDs. Took him like three years but he was eventually able to make a chip with a 20 micron process using a microscope and a UV DMD development board [1]. He did have access to wire bonders, IC debugging equipment, professors, etc though.
See if you can get a plasma window for that vacuum chamber, which will allow you to do e-beam etching down to about 100nm with the wafer outside of the chamber. Combine it with a DIY 80/20 class 100 cleanroom (if you can make it small enough to be able to manipulate it with isolated gloves then it will be relatively cheap), some precise X-Y linear stages (you can probably get away with +-10nm precision at 100nm), supersonic bath with etching fluid, and a high quality blender for applying the resist and VOILA you have a simple little fab. You can probably adopt some stuff from an SEM to scan the electron beam across the resist but you're probably better off trying to come up with a way of etching through a die long term (much more difficult and slow).
A friend at Caltech took this a step further and came up with his own crude SoC that took input from basic switches, did calculations based on code taken from a small off the shelf EEPROM, and displayed the output to segment LEDs. Took him like three years but he was eventually able to make a chip with a 20 micron process using a microscope and a UV DMD development board [1]. He did have access to wire bonders, IC debugging equipment, professors, etc though.
[1] http://ajp.aapt.org/resource/1/ajpias/v73/i10/p980_s1