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For Windows Search (that's content searching - its hopeless for file name searching) the main thing is to only index your data, have a look at the iFilters from Citeknet and the iFiltershop, and a get a decent iFilter for PDF - Adobe, Foxit or xChange all have them - I use the xChnage one because I use that viewer. The other thing is to run the indexing service at lowest priority you do that in the Services console.
Moving books is I/O bound. When you were moving those books your CPU was probably 90%+ idle. Do a ctrl/alt/esc, go to Performance Tab, click Resource Monitor, it gives a good overview of what's doing what.
It does seem a bit slow, are your libraries on the same drive as the system (I guess they would be on your laptop) - I keep my libraries on a second drive. Is the desktop MOBO SATA2 or SATA3, mines SATA 2 so its a bit slow.
It could be that your drive needs defragging - AFAIK Win7 defrags when its got nothing to do but I don't think its very aggressive. There are other defraggers that claim to get more oomph out of a drive, I think Pirifiorm (the cCleaner folks) might have one.
When you say the lost comments & tags are in the ebooks, do you mean they're embedded as metadata or they're in a book jacket - if they're embedded you might be able to get them back.
BR
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