I have a R33 GTR V-Spec which I purchased primarily stock about 4 months ago. Mine isn't a daily driver but I do expect to get it to the track and I'm looking for a very solid car before, at some time in the future, rebuilding the motor for big HP. A few of my thoughts.
You can spend a bit on suspension and brakes and get a good return. I have put on new brakes (Project Mu rotors, Nismo Pads, MCS, & braided lines and gotten a good braking improvement (around $2000).
I'm also dropping money into suspension. Take a look a the SK group buy. I'm actually only buying the stabalizer bars and camber/caster parts (around $1000 plus install). I think this will give the biggest bang for the buck as a GTR suspension isn't bad to begin with and this simply tightens it up, allows better alignment/tuning and improves handling. Even the cheapest coilovers will cost $1300 and it is doubtful you will get the same performance improvement, though if you want to lower your car this will allow that where what I have done won't.
I've added an Apexi intake ($400). Easy upgrade - and to be childish - I love in the intake sound.
Next is an external oil cooler with filter relo. Bot one from JJR for $400 but the cost will be in installing it. I understand the idea of running a sump baffle and why it is better but I'm not pulling the motor just for that, which is what you need to do. I've also put on a Nismo oil seperator ($400)
So I'm spending probably $4000-4500 including labor and have what I think is a very solid base car which stops and handles very well and should support track days w/o blowing up.
There are people here who can comment better on engine upgrades than I can.