I played Zelda at 900 mhz and its slow, you are saying 99% of fullspeed. I am saying more like 60% speed at its best.
As I said it depends on what sacrifices you will make for speed. I lowered my window width to 640. Yes it means I have black bars but the emulator isn't trying to do that funny rendering mode.
If you don't want to do that then enable the frame buffer and set it to 400 x 240.
Remember the N64 had a few different resolutions depending on the game, but it was usually 320 x 240, with the lowest res games being 286 x 220. Hi res was 640 x 480 (Rogue Squadron with expansion pak). Zelda OoT was 320 x 240.
For maximum performance at native resolution try the following in your gles2n64 plugin.
#gles2n64 Graphics Plugin for N64
#by Orkin / glN64 developers and Adventus.
config version=1
#These values are the physical pixel dimensions of
#your screen. They are only used for centering the
#window.
screen width=800
screen height=480
#The Window position and dimensions specify how and
#where the games will appear on the screen. Enabling
#Centre will ensure that the window is centered
#within the screen (overriding xpos/ypos).
window enable x11=1
window fullscreen=1
window centre=1
window xpos=0
window ypos=0
window width=640
window height=480
#Enabling offscreen frambuffering allows the resulting
#image to be upscaled to the window dimensions. The
#framebuffer dimensions specify the resolution which
#gles2n64 will render to.
framebuffer enable=1
framebuffer bilinear=0
framebuffer width=320
framebuffer height=240
#Frameskipping allows more CPU time be spent on other
#tasks than GPU emulation, but at the cost of a lower
#framerate.
frame render rate=1
#Vertical Sync Divider (0=No VSYNC, 1=60Hz, 2=30Hz, etc)
vertical sync=0
#These options enable different rendering paths, they
#can relieve pressure on the GPU / CPU.
enable fog=0
enable primitive z=1
enable lighting=1
enable alpha test=0
enable clipping=0
enable face culling=1
#Texture Bit Depth (0=force 16bit, 1=either 16/32bit, 2=force 32bit)
texture depth=1
texture mipmap=0
texture 2xSAI=0
texture force bilinear=0
texture max anisotropy=0
#
update mode=1
ignore offscreen rendering=0
force screen clear=0
use IA textures=0
Be warned though there will be jaggies and a black bars on each side.