I recently purchased a Mayflash N64 adapter for my PC because it's easier for me to stream on an emulator than on my N64. I calibrated the controller so the joystick and everything is great, the only problem im having is with the A button having a bit of input lag so when i try to do tricks like say bomb clip i wont double jump. Anyone have a way of fixing this?

i have the same adapter but not this problem try to put the controller in to the second player and calibrate the Z stick with the Z button :)

From what I know Mayflash adapter has about 24 ms of lag in worst case. You should play on N64 if you have it, since it is superior to emulation. If you insist on playing on it then get a better adapter, currently the best option would be third version of N64 to USB by raphnet: http://www.raphnet-tech.com/products/n64_usb_adapter_gen3/index.php