Ok update time. I have successfully combined both of the world together using MCEdit. The issues with the orientation of the blocks was caused by me rotating the schematic of the world when I was combining together. I do however still have one issue remaining. In the past I have used VoxelSniper to make the world look natural and not like the world was simply copied and pasted. I tried installing VoxelSniper and BukkitForge but it won't let me edit blocks that are at a far distance, making it impossible to terraform properly. Does anyone know a solution to fix this or perhaps another mod that can be added to make the combined worlds look seamless?