Is it possible to install an aftermarket top mount inter cooler and a aftermarket cold air intake? (04 STi)?

There is no reason why not. Now if you meant a front mount, there are only one or two on the market that work with a cold air intake but a top mount will not get in the way. Make sure you get tuned for those if you do decide to do them. Especially the inter cooler. On an 04, you will probably run fine without tuning and possibly even feel some gains but tuning will make a huge difference.