Re fragmentation: yes, the tendency to fragment is related to the amount of free disk space, so if the Linux installation took space on that disk, I'm not surprised it fragments more.
To get rid of Linux, the main thing would be to claw the disk space back by using the partitoning tool of your choice - or re-installing Windows. You might be able to use the Linux partitioning tool, by pretending to start another Linux installation, but using it in manual mode and telling it to do what you want. If you don't reinstall Windows, you probably have to live with the Linux "boot loader"; you could get rid of it, but you don't have to if it works and loads Windows as it should.
Re file sharing between the systems: the way I would go about it would be to designate the most powerful machine, with the most disk space, as a "server", and have every other "client" machine talk to that. Rather that than have "everyone talking to everyone else", which could get over-complicated. Assuming that's the Windows desktop machine, you can just use standard Windows Sharing. On the Linux machine(s), you'd install "Samba Client" components, and "connect to server -> SMB or Windows" from the menus.
Optional: if your server is a Linux box, you could install the Samba Server, to make it act like a Windows server, though that can get a bit fiddly. An alternative is to install the OpenSSH Server there and OpenSSH clients on the Linux boxes. To do file transfer across SSH, you use the Linux command line, or a more friendly SCP (SSH Copy) program, such as
WinSCP (Windows) and similar ones running under the Ubuntu graphical interface (search the repository).
(Personally, I've gone the other way: I installed the
Cygwin OpenSSH Server on the Windows "server" I use, and back up my Linux netbook to that using a program called
Unison. It's solid now, and transparent, but OpenSSH and Unison need a bit of fiddling to work smoothly without entering passwords every time.)