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I got it to work! First, thank you so much for you help Yal! Your help has cleared up a bunch and made it so I could figure this out. It took a bit to try and understand how the menus work, and I still don't get it all, but for those interested in getting the mouse to work, here's what I did:

First, in the init_input script I added:

#macro input_MA 9
#macro input_MB 10
#macro INPUT_MAX 11
global.input_key[input_MA] = mb_left
global.input_key[input_MB] = mb_right

Then in the function get_keys script I added and changed a couple lines:

p_a = ((p_a + 1)*(k_a + k_ma))
p_b = ((p_b + 1)*(k_b + k_mb))
k_ma = mouse_check_button(global.input_key[input_MA])
k_mb = mouse_check_button(global.input_key[input_MB])

Then I found pretty much everywhere that k_a was and made it (k_a||k_ma). And the same thing with k_b,  I changed them to (k_b||k_mb).

This was to allow for the mouse button to work as the 'A' or the 'B' button, while still keeping the regular 'A' and 'B' button working. So you can use either the mouse or the keyboard.

The part that I had trouble with was figuring out which menu box the mouse was in. What I ended up doing was looping through the options to see if the mouse was hovering over an option. Than looping through the options and checking if the mouse was in each rectangle until it found the right one. It's on the more expensive end, it requires a few loops, but it does seem to work, and I haven't noticed any issues.

So, here's what I put, right near the end of ggui_menu_handler (just above the closing }):

for(c = 0; c < ggui_frames;c++){
     //check to see if the mouse is hovering over an option
     if(mouse_x > ggui_frame_l[c] && mouse_x < ggui_frame_l[c] + ggui_frame_w[c]){
     if(mouse_y > ggui_frame_t[c] && mouse_y < ggui_frame_t[c] + ggui_frame_h[c]){
          //the mouse is hovering over an option, so loop through the options to find out which one we are over
          for(var d = 0; d < menu_w; d++){
          for(var e = 0; e < menu_h; e++){
               frame = menu_frame[d, e];
               //here we are checking to see if the mouse overlaps with the rectangle created by the menu option
               if point_in_rectangle(
                 mouse_x, 
                 mouse_y,
                 lerp(ggui_frame_l[frame],ggui_frame_l[frame] + ggui_frame_w[frame],menu_reg_l[d, e]),
                 lerp(ggui_frame_t[frame],ggui_frame_t[frame] + ggui_frame_h[frame],menu_reg_t[d, e]),
                 lerp(ggui_frame_l[frame],ggui_frame_l[frame] + ggui_frame_w[frame],menu_reg_r[d, e]),
                 lerp(ggui_frame_t[frame],ggui_frame_t[frame] + ggui_frame_h[frame],menu_reg_b[d, e])
               )
               {
                    menuvalue_x = d;
                    menuvalue_y = e;
                    break;//End when we find the first option that matches
               }
          }
          }
     }
     }
}

If anyone has a way to refine this and make it less slow and costly, I'd love to hear it. If what I have put above is unclear, let me know. But, this is what I did, and the mouse seems to be working well.

Hello again. I've been trying to get mouse controls to work. I managed to get the mouse buttons working no problem, but I'm having a fair bit of trouble getting the menu to figure out which menuvalue_x and y the mouse should be on. I tried the code above, and it only seemed to partially work. On the main menu it only every selects New Game. On the player name select it goes to 'M' immediately, then if you click it selects all the letters from A-L.

I also tried a different system where I defined some variables and used them to figure out the menuvalue_x and menuvalue_y. The variables I used:

var mouse_y_gui = device_mouse_y_to_gui(0);
var mouse_x_gui = device_mouse_x_to_gui(0);
var array_l = array_length(ggui_frame_l) -1;
var array_w = array_length(ggui_frame_w) -1;
var array_t = array_length(ggui_frame_t) -1;
var array_h = array_length(ggui_frame_h) -1;
var menu_width = ggui_frame_l[array_l] + ggui_frame_w[array_w];
var menu_height = ggui_frame_t[array_t] + ggui_frame_h[array_h];
var menu_x = ggui_frame_l[0];
var menu_y = ggui_frame_t[0];

to try and get this code to work:

if((mouse_x_gui > menu_x && mouse_x_gui < menu_x + menu_width) && (mouse_y_gui > menu_y && mouse_y_gui < menu_y + menu_height))
{
menuvalue_x = floor(mouse_x_gui - menu_x/(menu_width/menu_w));
menuvalue_y = floor(mouse_x_gui - menu_x/(menu_width/menu_w));
}

I'm not quite sure what I missed, but it would be great to get mouse controls working, and any help would be greatly appreciated.

Thanks so much for all the info! Looks like it should be manageable and a good place to get started.

Hey, I've been looking to create a monster collection game, and this looks like it might be a great base to start with, but I had some questions. I'm planning on using a simplified grid battle format, so battles would take place across a 4x3 grid. Is this something that would be implementable without absolutely tearing the code base apart? There are a fair number of other changes I would be making to the traditional battle system as well, including creatures being able to potentially learn more than four moves, moves that can be powered up, and more, but I think the grid is the biggest change. Is this engine flexible enough to handle those sorts of large system changes, or would I be better off starting from scratch (or with a different engine)? Either way, this seems like a great engine, it's really cool to see something like it created to help others.