To move the boot system away from the 100mb partition, you need to put the boot files/system on the other partition and then make that partition active.
To add the boot files, I think you use the BCDBOOT command. If you look for hidden, system files, the boot folder should be in the System Reserved Partition. You need to add that and the other boot files to the primary partition.
Something like bcdboot C:\Windows /s C: if C: is the Windows Partition. After you do this using an administrative command window, check to make sure the Boot folder is on that partition. You can check Microsoft for the commands if you like.
Once you get your system booting the the Windows partition, you can use something like Partition Wizard to...