So, the Ghost is not at all a rigger or pilot, and is a pure street samurai, which is why the lack of matrix stuff.
In your case: I think there are four reasonable ways to go. Keep in mind that your helicopter doesn't need to be very good at flying in order to handle basic stuff.
a) Be a decent-ish hacker on the side. This actually isn't too hard but might stretch you too thin. The more things you want to cover the more harsh and merciless you have to be about trimming the fluff. See the Generalist and the Mercenary Rigger for examples of triple-role characters. Once you have the stuff you need to be a hacker, you can also be a meh OK command rigger for no real investment and that lets you do stuff like Command-rig your copter to pick you up and the like.
b) Make your helicopter good at doing things on its own. This means upgrading its pilot, firewall, response, getting autosofts, getting an Agent to protect it from hackers, etc. This is going to be expensive and might again be more than you can afford. You cannot do this halfway - if you upgrade it so it's good at flying itself but lacks matrix defenses, it will get WTFPwnt by enemy hackers.
c) Just say no to wireless. Turn it off and fly manually. You can always turn on the wireless again if you absolutely have to for some reason. The pilot it comes with is going to be good enough to do stuff like pick you up, but not good enough to do stuff like fight on its own, and it will be wtfpwnt by anyone who knows how to hack.
d) Is there a hacker in your group? Turn the wireless off when you are in the chopper, and if you aren't in the chopper, slave it to the hacker's commlink.
Being half a hacker is worthless. You can either deal with matrix stuff or not deal with it; there's no real point in being able to suck at it.
Re: Powers, I would suggest getting a Geas on one of your powers to shave off that last little bit. Cerebral Boosters 2 is +2 logic, Keen Wits is +1. Choosing Keen Wits over Cerebral Boosters is pretty silly. My suggestion would be to either Geas your Improved Reflexes (which would knock it down to 1.25, leaving you .5 PP for other stuff), or Geas your Keen Wits (which would knock it down to .625, leaving you at exactly 4). The draw of the latter option is that if your Geas does get violated, you only lose 1 logic until you fix it, which is not as critical as your IPs.