I can't stress this enough, keep your private and enterprise cloud behind a vpn. Especially if you are a part time Admin with limited resources. Sooner or later you will be hacked.
Pretty sure thats not a limitation of aria2. What system are you using? There a multiple options:
Just build a queue
Check if aria2 locks up because of system limitations. Max open files, max concurrent connections (there will be a practical limit no matter what you do)
build a queue with a cluster to overcome such limitations