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1) What about physical files? How would they be copied?
They
would not be copied.
They would be created and loaded by the new MySQL instance running on the new machine. This is especially relevant if you're moving to a different version of MySQL.
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2) Would mysqldump take all procedures,functions,triggers,grants etc backup as well?
Yes.
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3) What about system databases? Do i Need to backup them as well?
Not for
this exercise, because the new instance will have its own system databases.
However you
should, of course, be backing up
all your databases, system or otherwise, in case you ever need to recover them. :-)
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4) Any specific considerations w.r.t. innodb or myISAM tables?
None at all.
Regards, Phill W.