Basically there are two explanations for this phenomenon:
(A) The statistical one
Just by random fluctuation, the individual chunks are not equally distributed in the network. You download a chunk faster, the better spread it is. Therefore, the rarest chunks have a pretty good probability of winding up as the last to-be-downloaded chunks. Since it takes longer to download them, you get the subjective impression that amule slows down towards the end of finishing a file.
(B) The uploaders of corrupted data one
Recently, there have been more and more clients on the network that intentionally upload junk to corrupt your downloads. You know that you are affected by this phenomenon if you get a number of "Part x is corrupted..." messages in amule's log. The effect of these malicious clients gets much worse towards the end of completing a file. aMule has some basic corruption handling against this but the affected downloads are still considerably slowed down.
In short:
If you get those "Part x is corrupted..." messages you can try to figure out who is responsible and manually block these guys in your firewall (which is quite tedious but it does help).
If not, I guess you just have to be patient.
In terms of taking the files prematurely out of the temp folder, I would be a bit careful about that. If the files are only slightly damaged or completely broken probably depends mostly on the file format: many movie formats are relatively forgiving, with rar and zip files you are often able to extract some of the content, and files like pdf I think don't respond well to this at all.
In any case, if you are doing this, I would strongly encourage you to *copy* the file out of the temp folder instead of moving it, so that you will also get a completely intact version of your file eventually...
