You can go one of two ways... either work on getting more power, or work on getting the power you already have to work for you.
Having the 5 speed is a big plus for getting power to the ground, but there are still things you can do. Consider a change of diff ratio to 3.5:1 or 3.7:1, or if you arent afraid of revving the guts out of it to cruise on the highway, then 3.9:1. This will give you better acceleration.
You can also work on making the engine produce more power, the best way being to improve flow. I see you've already gone with significant improvements on the exhaust and intake side of things, so its probably time to get a little more "internal" about it. At this point I would be considering either a cam upgrade (which would negate your performance chip i'm afraid) or a cheaper option (which I would go with personally) is to install high ratio rockers from F.I.T. or Yella Terra. That'll increase valve lift (but not duration like a cam would) and your flow into and out of the head will be greatly improved. This will have most benefit at the top of the rev range. Cost is approximately $800 if you install yourself. (Very easy... even I would do it myself and I'm no expert)
EDIT: please take my comments about the revs with a 3.9:1 diff with a grain of salt as I just realised of course the ratios are different in a manual and you have an extra gear to work with anyway...
