I did both in 2015 but had Kevin rather than Haley for 3903 so I'm not sure if the course would have changed. I would recommend doing both since you'll need 3903 if you intend on doing an applied microeconomics thesis and you'll need 3904 if you intend on doing an applied macroeconomics thesis. The problem is that it's unlikely that you truly know what an applied thesis is until you've done these subjects (unless you've done some RA work), so I really recommend doing both.
If you are truly indifferent between applied micro and macro and you can really only do 1 then I would do 3903. 3903 was probably my favourite subject in university (but mostly because of Kevin who is now not taking the course) and it was much easier than 3904 imo (but others disagreed). Most importantly though, the way the subjects are currently for Honours, 3903 is more relevant than 3904 for the actual coursework (assuming the subjects don't change). I found 3903 helped alot in assessments during my Honours year while 3904 only had minimal benefit. Also, Ed is one of the best (if not the best) researchers in the department, but his lecturing style is an 'acquired taste' to say the least.
@elkedag, might be too late but BEc/LLB will allow you to do both if you can make the switch.