I made an customized version of Ubuntu 10.04 LTS with my required software, but after customization,
wubi.exe does not work. Any idea how to make it work again?
The Wubi Customization section in the official Wubi Guide contains some hints and tips.
The guide also talks about customizing Wubi itself and using Wubi for non-Ubuntu distributions, so I have included the points I think are most relevant for your needs/problem, along with my comments: