Get a J&J Performance Ceramic barrel in either 14" or 16". Then you have an awesome barrel that can be upgraded to APEX with their little adapter that they make. Stock APEX barrels are crap so start off with a JJ. You can usually get them for around $35 on eBay.
Get a low profile hopper for your Cyclone.
Remote as FreeEnterprise said. Tippmann makes one called the Connex which allows you to disconnect from your gun under pressure, Guerilla Air makes one called the Cobra Coil. Basically they are ProConnect 3 fittings which are awesome. http://www.ansgear.com/Tippmann_Conn...remoteline.htm
Dont mess with internal upgrades. No power tubes, not bolts. THe only internal upgrade I would recommend is the Engler Light Rear Bolt. http://www.englercpb.com/zencart/ind...ducts _id=945