Decisions. Decisions.
You will always want more. Keep that in mind. If you spend 2-3k now on Stage 2+, you will want to spend 2-3k a year from now on Stage 3 big turbo. It's just the nature of car enthusiasts, we always want more after we get used to what we have.
I went APR Stage II and can honestly say I have no desire to upgrade to IS38. If I had a choice to do it over again, I'd probably go JB4+Downpipe and leave it at that.
Definitely purchase an exhaust or have one custom made. It completely changes the experience and you might not even desire more power.
My recommendation is go APR Stage II. You'll feel quite a bump and not break the bank. I don't run an upgraded IC or an expensive exhaust. But I do suffer from heatsoak. But there you can save at least $1200. It's all about how much you want to splurge. I mean if I were to upgrade the turbo, I'd probably go big turbo, to feel that massive difference for all the money spent. If I went IS38, it would probably feel like when I went APR Stage I the first time. But after a while, just like with Stage I, I'll want more.
Let us know what you decide to do!