ok so I figured out how to compile mame and was able to enable the hi-score + remove all warning screens. One of the major things with light guns that everyone talks about is making sure the Force Direct Input is not enabled. You must make sure there is no check mark under the build tab in Mame Compiler 64 when compiling mame otherwise you will get weird things happening with light guns in mame.
I am using the dos version of mame 0.149 and using 2 aimtrak light guns with out any issues. I configured the light guns in the input general options in mame and both guns were set for all gun games in mame. The only thing that will have to be setup would be the trigger button and in some cases like in time crisis you would also need to configure the foot pedal.
If anyone knows how to default the trigger button to all the light gun games please let me know. From what I have experienced each game is different and each games has its own config so Im thinking there would be no way in doing this.
I used this site for compiling mame.
http://headsoft.com.au/index.php?category=mame&page=mc64 I pretty much followed these instuctions and everything seems to be working great. I did not update my verison of mame the only update I applied to the mame binary was the hi_149.txt. After compiling mame I created my mame.ini and edited some settings.
Another issue that I came across was that my guns ids were gun2 for player1 and gun3 for player2. If you want your guns to show up as Gun 1 and Gun 2 you must unplug your mouse or any other devices that act as a mouse like a trackball etc... then go into the aimtrak software and reset your ids to your guns. Once you do that the guns should now have the correct ids.
In the mame.ini these are the settings I changed to get my guns to work.
#
# CORE INPUT OPTIONS
#
coin_lockout 1
ctrlr
mouse 1
joystick 0
lightgun 1
multikeyboard 0
multimouse 0
steadykey 0
ui_active 0
offscreen_reload 0
joystick_map auto
joystick_deadzone 0.3
joystick_saturation 0.85
natural 0
joystick_contradictory 0
coin_impulse 0
#
# CORE INPUT AUTOMATIC ENABLE OPTIONS
#
paddle_device keyboard
adstick_device lightgun
pedal_device keyboard
dial_device keyboard
trackball_device keyboard
lightgun_device lightgun
positional_device keyboard
mouse_device keyboard
#
# INPUT DEVICE OPTIONS
#
dual_lightgun 2
The dual lightgun option I tried putting a 1 there but mame did not like it. If someone else has an idea to why please let me know.
Everything is working great and I am very thankful for the people that pointed me in the right direction.