I have built clisp 2.29 in my cygwin environment with gcc 2.95, gcc 3.2 and
without major problems (although I had to add -falign-functions=4 for gcc
3.x and gcc 3.2 wouldn't work with safety less than 2).
Do you have full cygwin? Why don't you simply use ./configure <directory-path>?
I reckon that the configure is slow, I think even slower than the actual build
If you have full cygwin I could offer pre-built binaries