This problem has been affecting me for the past 3 years, on and off.
However, in the past 6 months, it has become worse. Before, a good rest
would suffice but nowadays I wake up with the image seperation at its
greatest.

I went to a ophthalmologist and he diagnosed it as squint and said
surgery was the only option since prisms won't work for my diplopia
which is measured at 18 dioptres. He also told me that surgery wasn't
100% and would require prisms to correct the rest. I immediately backed
out after that and currently waiting to see another doctor.

But is it really squint or "brain-diplopia"? My eye seem to look
straight and no one can tell if they are deviating. With enough effort
I can fuse the images into one (sometimes I can't), usually for a
couple of seconds and the seperation of images vary during the day and
gets worse during the night. The seperation is side by side and affects
me only when I try to see something more 5 feet away. I do a lot of
near work and stay up late quite often and wonder if it has taken a
toll on my sight.