Your problem description is not very clear, but I'll try to answer some of it the best I can:
1. 2 swaps are not necessary. 1 swap is all you need (if it's large enough - raw ram x 2). Whichever swap is closer to the "0" point in gparted keep that one. Open a terminal and # sudo bilkid /dev/sda2 (or relevant number) will give you the UUID of the swap you want to keep. Open the /etc/fstab of both systems and see which one has the incorrect (second) UUID. Replace with correct UUID & save. #swapoff then #swapon -a. You can now delete swap2 from gparted.
2. What do you mean by "boot partition"? Do you mean separate partition for /boot where grub files reside? If so, it is a good idea to put it on a separate partition. You can place this at the very end of the disk and 300-400 MB's are enough size. Create the partition, mount it (like /mnt) and copy all what's under both /boots to the new partition. Then rename /boot for active system create a new /boot, unmount /mnt and re-mount to /boot. Now run # sudo grub-install /dev/sda (assuming disk in question is sda). Delete the other systems /boot contents and edit both /etc/fstabs to auto-mount /boot partition by UUID. For good measure, copy original /boot/grub/grub.cfg somewhere (like desktop) before you do all this. Compare the old cfg with the new one. If a new one was not created, run # grub-mkconfig
3. It's unclear which partition you want to truecrypt, but I would advise against it until you become more comfortable with linux because if you run into some difficulty you will have a tough time retrieving your data and others will not be able to help you so easily.