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What brand are the controllers? Some are easier to do shorthops/tilts than others. Under settings, try a different emulator plugin in Project 64. If your controllers aren't that good, they may not have the level of sensitivity. Try different joysticks and buttons on the controllers, it doesn't matter which buttons go where as long as your happy with the controls. If they still don't work correctly, it's probably the controller just not being made for more precise inputs. You can probably return them and get a different controller, or a usb adapter for an N64 controller.
My favorite controller for Smash is a wired Xbox 360 Controller. The buttons numerous and of great quality, and it feels nice in the hand. I ordered mine from here: You can also likely find it in a local Walmart. It comes with an installation CD so drivers are not an issue. If you already have a wireless one, you can also look for a usb adapter. Here's the link to the wired 360 controller.
http://www.walmart.com/ip/Microsoft-Wired-Controller-Chill-White-Xbox-360-Xbox-360/4196264
Here is the adapter for an N64 controller. The problem with N64 controllers is the joystick. It's easily worn out over time rendering it very difficult to use. I have the original N64 console, Smash 64 cartridge, and 4 Nintendo controllers, but I cannot play nearly as well as I do with them as I can with the 360 Controller.
http://www.amazon.com/Nintendo-64-N...dp_top_cm_cr_acr_txt?ie=UTF8&showViewpoints=1
If you have more questions, ask
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