upgrade to media server5

What do you mean by upgrade? Do you mean free upgrade...in that case i do not think  upgrade to AMS 5 from FMS 3.5 is for free.

If you mean upgrade in terms of config files and assets(and your custom applications)... I guess once you install AMS 5, most likely same applications and assets should work.However as for config files, since there have been some significant changes between AMS 3.5 and AMS 5, i would suggest you to manually port those changes ...However IMHO, in most cases the transition from 3.5 to AMS 5.0 should be smooth...Apart from the fact that FMS 3.5 is out of support, you should also look as to what are your specific mileages from moving to AMS 5.0.Please look at the product web page for details.

Aside to that, i would also like to mention that AMS is available at AWS market place.