It seems to me that you describe 3 fields of western scholarship (all intertwined, but we can still analyze them separately to some extent) that developed in the 19th century and continue to influence western attitudes toward Islam and Muslims: comparative religion, philology, and "Orientalism" of the kind that served western imperial power structures.
So separate out all of the material about EACH of these and combine EACH into a section of the paper.
Then connect EACH to its continuing influence on attitudes today. This may mean leaving OUT some of the material about today, as well-perhaps some things in today's discourse came from other places.
I've highlighted the parts of the paper that seem to me to correspond to each section.
Introduction: 19th-century ideas about Islam still influencing attitudes today. This can be seen in 3 broad areas:
1. The study of comparative religion, with its way of setting up Christianity as normative.
2. The study of language and linguistics (philology) with its granting of superiority to "Indo-European" languages
a. And then drawing implications about the superiority of "racial" groups based on their languages.
3. "Oriental" scholarship in the service of western imperial ideas.
Results: today's stereotypes of Muslims as
1. Religion/theology: rigid, legalistic, fear rather than love, not universal, national, etc.
a. Especially violent
2. Language/thought: again rigid, etc.
3. Politics: Islamic civilizations incapable of understanding democracy, etc.
There is one additional issue here: from page 24 on, you change to a different kind of structure. I think (though it's not always clear) that you set out here to show a few cases where a 19th-century scholar said XXX and we can see those ideas reflected in a contemporary writer who says the same thing.
The problem is that this is a completely different structure than the first part of the paper pursued. I think maybe this means that these examples should somehow be integrated into the structure above. That is, Plucinski and Saraswati would go with the other 19th-century writers discussed in the first part of the paper and Spencer and other contemporary writers would go with the second section.
And again, keep in mind that perhaps not everything the contemporary authors say comes from the 19th-century sources; it can come from other places, in which case it doesn't have to be mentioned in your paper. It's not relevant to your case. Anyway, think about how these cases might be integrated better with the rest of the paper.