Yes, this is a main pain PY and I have dealt with since time immorial.
Sometimes I wanted to yell at my computer "No, you find sysvars2.21.txt!"
What I ended up doing is wherever the program sets up MainDir (it's a variable) I check to see if the left most bit is "C:\darwinsource" cause that's where I keep the source codes. If it is, I delete that bit and set it equal to: "C:\DarwinbotsII\" cause that's where I keep my DB install.
Somethign similar should work for you, but it takes a bit of finagling to set it straight. Feel free to downlaod 2.4's source and see how I did it.