Wubi is windows Ubuntu installer which installs Ubuntu as a program inside your windows system and usually on the same partition, AFAIK.
If you have the option to boot Ubuntu or windows then you have installed the Ubuntu bootloader to the master boot record (unless you manually configured the windows bootloader??)
Ubuntu bombs again is not very informative. More details on what happens when you select Ubuntu? Which bootloader are you using?
My understanding is that you would need to install some third party software on windows to read/write Ubuntu files as microsoft does not have any software for this purpose by default.
If you did a wubi install and if you are using the Ubuntu bootloader and if you then remove Ubuntu from windows, you will be unable to boot windows. So first, do you have a windows installation CD/DVD to reinstall the windows bootloader to the master boot record?
I think the best first step would be to go to the site below, read the instructions, download the bootinfoscript, run it from any Linux Live CD terminal and post the output here:
Doing that will give us detailed information on your drives/partitions and boot files and allow someone to make a more specific suggestion.