Yeah, to make a new connection each run, move the connect to inside the go loop. To use new connection info for each connection, make them shared varaibles. Like:

my $user:shared = 'jlahowet';                                         
+                           
my $server:shared = 'mistral.unl.edu';                                
+                           
my $lcl:shared = '/home/deadpickle/Desktop/Virtual Cockpit/uavposition
+';                         
my $rmt:shared = '/home/jlahowet/UAV/COORDS/uavposition';  

#my $thr = threads->new(\&sftp, @setup);
my $thr = threads->new(\&sftp);


#then in your thread-code use the shared vars instead of
#using the passed in @setup array
[download]

You already have your entry widgets to setup to automatically change the vars with -textvariable. There is one thing to watch out for: sometimes the threads will not automatically pick up changes in textvariables, you might have to manually read them, but try it first, you may get lucky.