I listed the previous comment what shortcuts add the 0001-Port-to-GMenuModel-and-add-menu-bar.patch patch file.
Now, look what shortcuts to remove the 0002-Remove-gtk_application_set_accels_for_actions.patch patch file:
Index: evince-3.10.3/shell/ev-application.c
===================================================================
--- evince-3.10.3.orig/shell/ev-application.c	2014-02-07 14:01:07.235558100 +0000
+++ evince-3.10.3/shell/ev-application.c	2014-02-07 14:01:07.231558100 +0000
@@ -1104,47 +1104,9 @@
                 { "help", app_help_cb, NULL, NULL, NULL },
         };
 
-        const gchar *action_accels[] = {
-          "app.open",                   "<Ctrl>O", NULL,
-          "win.open-copy",              "<Ctrl>N", NULL,
-          "win.save-copy",              "<Ctrl>S", NULL,
-          "win.print",                  "<Ctrl>P", NULL,
-          "win.copy",                   "<Ctrl>C", "<Ctrl>Insert", NULL,
-          "win.select-all",             "<Ctrl>A", NULL,
-          "win.save-settings",          "<Ctrl>T", NULL,
-          "win.go-first-page",          "<Ctrl>Home", NULL,
-          "win.go-last-page",           "<Ctrl>End", NULL,
-          "win.add-bookmark",           "<Ctrl>D", NULL,
-          "win.close",                  "<Ctrl>W", NULL,
-          "win.escape",                 "Escape", NULL,
-          "win.find",                   "<Ctrl>F", "slash", NULL,
-          "win.find-next",              "<Ctrl>G", NULL,
-          "win.find-previous",          "<Ctrl><Shift>G", NULL,
-          "win.select-page",            "<Ctrl>L", NULL,
-          "win.go-backward",            "<Shift>Page_Up", NULL,
-          "win.go-forward",             "<Shift>Page_Down", NULL,
-          "win.go-next-page",           "n", NULL,
-          "win.go-previous-page",       "p", NULL,
-          "win.sizing-mode::fit-page",  "f", NULL,
-          "win.sizing-mode::fit-width", "w", NULL,
-          "win.open-menu",              "F10", NULL,
-          "win.caret-navigation",       "F7", NULL,
-          "win.zoom-in",                "plus", "<Ctrl>plus", "KP_Add", "<Ctrl>KP_Add", NULL,
-          "win.zoom-out",               "minus", "<Ctrl>minus", "KP_Subtract", "<Ctrl>KP_Subtract", NULL,
-          "win.show-side-pane",         "F9", NULL,
-          "win.fullscreen",             "F11", NULL,
-          "win.presentation",           "F5", NULL,
-          "win.rotate-left",            "<Ctrl>Left", NULL,
-          "win.rotate-right",           "<Ctrl>Right", NULL,
-          "win.inverted-colors",        "<Ctrl>I", NULL,
-          "win.reload",                 "<Ctrl>R", NULL,
-          NULL

After this shortcuts remove part you adding following accelerators:
+            gtk_application_add_accelerator (GTK_APPLICATION (application), "<Ctrl>F", "win.find", NULL);
+
             gtk_application_set_app_menu (GTK_APPLICATION (application),
                                           G_MENU_MODEL (gtk_builder_get_object (builder, "appmenu")));
           }
 
-        g_object_unref (builder);
+        gtk_application_add_accelerator (GTK_APPLICATION (application), "F7", "win.caret-navigation", NULL);
 

The shell/menus.ui file you added following accelerators:
       <item>
         <attribute name="label" translatable="yes">_Open</attribute>
         <attribute name="action">app.open</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;O</attribute>
       </item>
     </section>
     <section>
@@ -33,6 +34,7 @@
       <item>
         <attribute name="label" translatable="yes">_Help</attribute>
         <attribute name="action">app.help</attribute>
+        <attribute name="accel">F1</attribute>
       </item>
     </section>
   </menu>
@@ -52,36 +54,43 @@
       <item>
         <attribute name="label" translatable="yes">Side _Pane</attribute>
         <attribute name="action">win.show-side-pane</attribute>
+        <attribute name="accel">F9</attribute>
       </item>
     </section>
     <section>
       <item>
         <attribute name="label" translatable="yes">_Fullscreen</attribute>
         <attribute name="action">win.fullscreen</attribute>
+        <attribute name="accel">F11</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">Pre_sentation</attribute>
         <attribute name="action">win.presentation</attribute>
+        <attribute name="accel">F5</attribute>
       </item>
     </section>
     <section>
       <item>
         <attribute name="label" translatable="yes">Rotate _Left</attribute>
         <attribute name="action">win.rotate-left</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;Left</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">Rotate _Right</attribute>
         <attribute name="action">win.rotate-right</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;Right</attribute>
       </item>
     </section>
     <section>
       <item>
         <attribute name="label" translatable="yes">Zoom _In</attribute>
         <attribute name="action">win.zoom-in</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;plus</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">Zoom _Out</attribute>
         <attribute name="action">win.zoom-out</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;minus</attribute>
       </item>
     </section>
     <section>
@@ -92,12 +101,14 @@
       <item>
         <attribute name="label" translatable="yes">_Inverted Colors</attribute>
         <attribute name="action">win.inverted-colors</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;I</attribute>
       </item>
     </section>
     <section>
       <item>
         <attribute name="label" translatable="yes">_Reload</attribute>
         <attribute name="action">win.reload</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;R</attribute>
       </item>
     </section>
   </menu>
@@ -107,10 +118,12 @@
       <item>
         <attribute name="label" translatable="yes">_Open…</attribute>
         <attribute name="action">app.open</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;O</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">Op_en a Copy</attribute>
         <attribute name="action">win.open-copy</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;N</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">_Recent</attribute>
@@ -120,6 +133,7 @@
       <item>
         <attribute name="label" translatable="yes">_Save a Copy…</attribute>
         <attribute name="action">win.save-copy</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;S</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">Send _To…</attribute>
@@ -132,22 +146,26 @@
       <item>
         <attribute name="label" translatable="yes">_Print…</attribute>
         <attribute name="action">win.print</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;P</attribute>
       </item>
     </section>
     <section>
       <item>
         <attribute name="label" translatable="yes">P_roperties…</attribute>
         <attribute name="action">win.show-properties</attribute>
+        <attribute name="accel">&lt;Alt&gt;Return</attribute>
       </item>
     </section>
     <section>
       <item>
         <attribute name="label" translatable="yes">_Copy</attribute>
         <attribute name="action">win.copy</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;C</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">Select _All</attribute>
         <attribute name="action">win.select-all</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;A</attribute>
       </item>
     </section>
     <section>
@@ -160,22 +178,26 @@
       <item>
         <attribute name="label" translatable="yes">_First Page</attribute>
         <attribute name="action">win.go-first-page</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;Home</attribute>
       </item>
       <item>
         <attribute name="label" translatable="yes">_Last Page</attribute>
         <attribute name="action">win.go-last-page</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;End</attribute>
       </item>
     </section>
     <section id="bookmarks">
       <item>
         <attribute name="label" translatable="yes">_Add Bookmark</attribute>
         <attribute name="action">win.add-bookmark</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;D</attribute>
       </item>
     </section>
     <section>
       <item>
         <attribute name="label" translatable="yes">_Close</attribute>
         <attribute name="action">win.close</attribute>
+        <attribute name="accel">&lt;Ctrl&gt;W</attribute>
       </item>
     </section>

Note: CTRL+LEFT and CTRL+RIGHT keystrokes is normal word navigation keystrokes (goto next or previous word) if the caret navigation is enabled. Please not overwrite this general keystrokes if affecting this keystrokes the caret navigation. If future all accelerators will be working, not will be conflicting this two accelerators the general caret navigation keybindings?

Attila


     <section>