There are a bazillion write ups on this swap. I'd say do it, but before you dive into it do some Google searches on the topic and read as much as you can. There is alot of little things that need to be done to make it work, but it's very possible and pretty straight forward. And FWIW I'm doing a similar one, using the engine from an Aviator, into my 2000. But I started a thread for that.
2000 Mustang GT-Former giggle gas addict
1990 Mustang GT w/ Vortech V3
***resident gun idiot***