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Welcome to Mobileread!
One thing you might want to look into is how the Kindle handles pdf searches.
Kindle will search all its mobi format (.mobi, .prc, .azw) books for a given word or phrase.
So if I want to search for "feral horse" I can search all my mobi format books at once, and my Kindle makes a list of books in order of how many times the term occurs (say "Misty of Chincoteague" has it 14 times, "Wild Horses of the West" has it 12 times, "Feral Livestock: Problems And Solutions" has it 3 times and "Letters from the West" has it once, I'll see them listed in that order.) If I click on a title, I get a list of samples (about 3 lines of text) of each place "feral horse" occurs in that book.
However as I understand it, if these books were all in pdf format, it wouldn't work that way. I would have to enter each book, and then search just inside that book, so I'd have to search "Misty of Chincoteague" "Wild Horses of The West" etc one at a time. And if I forgot that "Letters From The West" had a mention of "feral horse" I'm out of luck, unless I enter and search every book just on spec.
Now, my understanding may be behind the times. Every year or so I go back and check, because the day the Kindle has cross-document search of pdfs is the day it becomes really useful for handling science papers. But I haven't checked recently.
But if you're planning to use a lot of pdfs, you might want to check this. Of course, if you're going to convert all your pdfs to .azw there should be no problem :-)
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