@Boabster
To make it easiest for you, you can take the settings from my .uae config and play with the settings a bit, but it should be set so that it will work well for you. 
It is best to create a backup before you make any changes to your .uae config. 
# UAE config for RunInUAE, which is designed to modify an existing working UAE config
# Use 3.1 Kickstart for Workbench, but allow ADF-booted games to still use an older Kickstart
kickstart_rom_file=AmigaOS4:Emulation/AmigaROMs/kick3.1.rom
#kickstart_rom_file=kick3.1.rom
immediate_blits=yes 
ppc.use_tbc=false
#JIT†compiller†settings 
cpu_type=68040 
cpu_speed=max 
cpu_compatible=false 
cpu_cycle_exact=false 
blitter_cycle_exact=false 
cachesize=8192 
#†memory†access†mode†direct†indirect=default†indirectKS†afterPic 
comp_constjump=true 
comp_trustbyte=indirect 
comp_trustword=indirect 
comp_trustlong=indirect 
comp_optimize=true
chipset=aga 
#collision†detection††none†sprites†playfields=default†full 
collision_level=none
chipmem_size=4 
bogomem_size=0 
fastmem_size=0 
z3mem_size=32 
gfxcard_size=32 
gfx_framerate=1 
gfx_width_windowed=800 
gfx_height_windowed=600 
gfx_width_fullscreen=800 
gfx_height_fullscreen=600 
gfx_lores=false 
gfx_linemode=double 
gfx_correct_aspect=false
gfx_center_horizontal=smart 
gfx_center_vertical=smart 
#show_leds=true 
gfx_fullscreen_amiga=false 
gfx_fullscreen_picasso=true 
sound_output=normal 
sound_frequency=44100 
sound_channels=stereo 
sound_bits=16 
joyport0=mouse 
joyport1=kbd2 
#SDL†specific 
#sdl.use_gl=true 
#AmigaOS†specific 
##screen†type†public†public†ask 
#amiga.screen_type=ask 
#amiga.publicscreen=<name> 
#amiga.use_dither=true 
#amiga.use_overlay=false
I left out the part with the hardfile configuration because you have to customize it for your setup anyway.
Let me know if it has had any effect on you 
