I found this hard to get my head around tbh, because I don't have your remote to match buttons to functions. So what I did was to make a test remote.conf using my numbers buttons, and test each keycode I didn't already know.
The ones I know (from my remote.conf) I just added to yours.
So here's what I came up with. It's in a different order (irrelevant, but you might want to tidy it up. There are probably mistakes in it - you'll no doubt find them. There are a whole bunch of buttons that are either not recognised at all by kodi or have no function attached to them.
The ones that aren't recognised - you'll need to change the linux keycodes (second column); ideally change them to something you'll use with the remote, otherwise you'll have a lot of keymapping to do.
repeat_enable = 1
repeat_delay = 40
repeat_peroid = 39
release_delay = 121
debug_enable = 1
fn_key_scancode = 0x00
left_key_scancode = 0x51
right_key_scancode = 0x50
up_key_scancode = 0x16
down_key_scancode = 0x1a
ok_key_scancode = 0x13
pageup_key_scancode = 0x55
pagedown_key_scancode = 0x54
mouse_begin
0 0x51
1 0x50
2 0x16
3 0x1a
mouse_end
key_begin
; Code Linux Linux description read in kodi as kodi keycode kodi action remote button
; ---- ----- ----------------- --------------- ------------ ----------- ------ ------
0x00 63 ;KEY_F5 f5 0xf094 61588 no action
0x01 11 ;KEY_0 61488 zero
0x02 395 ;?KEY_LIST??? XBMCK_UNKNOWN
0x03 127 ;KEY_COMPOSE leftwindows 0xf0d6 61654 no action
0x04 10 ;KEY_9 61497 nine
0x05 9 ;KEY_8 61496 eight
0x06 139 ;KEY_MENU menu 0xf0d8 61656 context menu
0x08 7 ;KEY_6 61494 six
0x09 6 ;KEY_5 61493 five
0x0a 133 ;KEY_COPY XBMCK_UNKNOWN
0x0c 4 ;KEY_3 61491 three
0x0d 3 ;KEY_2 61490 two
0x0e 136 ;KEY_FIND XBMCK_UNKNOWN
0x0f 186 ;KEY_F16 XBMCK_UNKNOWN
0x10 109 ;KEY_PAGEDOWN pagedown 0xf085 61573 pagedown
0x11 102 ;KEY_HOME home 0xf088 61576 FirstPage
0x13 97 ;KEY_RIGHTCTRL ctrl-rightctrl 0x1f0d1 127185 no action
0x16 103 ;KEY_UP 61568 up
0x18 104 ;KEY_PAGEUP pageup 0xf084 PageUp
0x19 15 ;KEY_TAB tab 0xf009 FullScreen
0x1a 108 ;KEY_DOWN 61569 down
0x40 116 ;KEY_POWER 61662 power
0x41 113 ;KEY_MUTE 61623 volume_mute
0x42 14 ;KEY_BACKSPACE 61448 backspace
0x43 183 ;KEY_F13 XBMCK_UNKNOWN
0x44 140 ;KEY_CALC XBMCK_UNKNOWN
0x45 130 ;KEY_PROPS XBMCK_UNKNOWN
0x46 8 ;KEY_7 61495 seven
0x48 138 ;KEY_HELP 0 (0xf200, obc-61697) no action
0x49 134 ;KEY_OPEN UNKNOWN
0x4a 5 ;KEY_4 61492 four
0x4c 125 ;KEY_LEFTMETA UNKNOWN
0x4d 70 ;KEY_SCROLLLOCK scrolllock 0xf0dc none
0x4e 2 ;KEY_1 61489 one
0x50 106 ;KEY_RIGHT 61571 right
0x51 105 ;KEY_LEFT 61570 left
0x52 128 ;KEY_LEFTMETA stop 0xf0bc Stop
0x54 120 ;KEY_SCALE UNKNOWN
0x55 121 ;KEY_KPCOMMA UNKNOWN
0x58 123 ;KEY_HANJA UNKNOWN
0x59 122 ;KEY_HANGEUL UNKNOWN
0x5a 119 ;KEY_PAUSE pause 0xf0dd none
key_end
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The ones that are recognised but not mapped to an action - you can either do as above (change the linux keycode) or make a keymap within kodi to map the code kodi reads to an action - see the link in my sig for some discussion / examples if you need them.
Then you'll need to work out which button corresponds to each command - ie you're linking the button to the code in the first column - and then swap them around to do what you want. Don't forget to add any repeats you want when you've finished (as per your original).
If you look in my remote.conf you'll see a bunch of linux keycodes that are already linked to kodi functions - use those to replace the ones you have that don't work.
My remote.conf:
# Pivos xios ds for harmony
factory_code = 0xbd020001
work_mode = 0
repeat_enable = 1
;repeat_delay = 40
repeat_delay = 100
;repeat_peroid = 39
repeat_peroid = 100
;release_delay = 150
release_delay = 100
debug_enable = 1
key_begin
; Code = IR keycode
; Linux = Linux keycode
; Android = Android keycode
; Button = Description button on remote
;
; Buttons with a * are not mapped to physical buttons on the harmonay remote.
;
; Code Linux Android key id kodi keymap kodi action My Harmony Harmony device command
; ---- ----- ------------- ------ ----------- ---- ------ ---------- ------- ------ -------
0xe3 30 ; A 61505 a custom (1) AudioDelay*
0xd8 70 ; EXPLORER 61660 scrolllock custom (2) Browser* - used to load tv channels groups keymap
0xd9 35 ; H 61512 h custom (3) CodecInfo* - used to launch tvguide groups keymap
0x90 111 ; DEL 61575 delete custom (4) Delete
0xd2 108 ; DPAD_DOWN 61569 down down arrow DirectionDown
0x99 105 ; DPAD_LEFT 61570 left left arrow DirectionLeft
0xc1 106 ; DPAD_RIGHT 61571 right right arrow DirectionRight
0xca 103 ; DPAD_UP 61568 up up arrow DirectionUp
0x84 33 ; F 61510 f ffwd FastForward
0x95 44 ; Z 61530 z custom (5) exit Return
;0x95 102 ; HOME 61622 backspace exit Return
0xc5 23 ; I 61513 i info Info
0xd6 46 ; MENU 61507 c menu Menu
0x80 113 ; VOLUME_MUTE 61623 volume_mute custom(6)favourites star Mute
0xe1 38 ; L 61516 l none NextSubtitle*
0xc2 52 ; . 61486 period SkipNext skip fwd NextTrack
0xce 28 ; DPAD_CENTER 61453 return Select ok Ok
0xcd 178 ; PAGE_DOWN 61573 pagedown PageDown channel down PageDown
0x9a 177 ; PAGE_UP 61572 pageup PageUp channel up PageUp
0x85 57 ; SPACE 61472 space Pause pause Pause
0x88 25 ; P 61520 pagedown Play play Play
0x45 116 ; POWER WAKE 61662 power XBMC.Shutdown() sleep PowerToggle (mapped to sleep by default in keyboard.xml)
0x96 51 ; , 61484 comma SkipPrevious skip back PreviousTrack
0xe4 16 ; Q 61521 q Queue-custom (7) run testscript Queue*
0xd0 14 ; BACK 61448 backspace Back prev Return
0xc3 19 ; R 61522 r Rewind rewind Rewind
0xe0 20 ; T 61524 t none ShowSubtitle*
0xe5 40 ; APOSTROPHE 61479 quote none SmallStepBack*
0x55 45 ; X 61528 x Stop stop Stop
0xe2 17 ; W 61527 w none ToggleWatched*
0x8c 114 ; VOLUME_DOWN 61624 volume_down VolumeDown none VolumeDown
0xdd 115 ; VOLUME_UP 61625 volume_up VolumeUp none VolumeUp
0x87 11 ; 0 61488 zero Number0 0 0
0x92 2 ; 1 61489 one Number1 1 1
0x93 3 ; 2 61490 two JumpSMS2 2 2
0xcc 4 ; 3 61491 three JumpSMS3 3 3
0x8e 5 ; 4 61492 four JumpSMS4 4 4
0x8f 6 ; 5 61493 five JumpSMS5 5 5
0xc8 7 ; 6 61494 six JumpSMS6 6 6
0x8a 8 ; 7 61495 seven JumpSMS7 7 7
0x8b 9 ; 8 61496 eight JumpSMS8 8 8
0xc4 10 ; 9 61497 nine JumpSMS9 9 9
key_end
repeat_key_begin
0xdd 115 ;VOLUME_UP
0x8c 114 ;VOLUME_DOWN
0x99 105 ;DPAD_LEFT
0xca 103 ;DPAD_UP
0xc1 106 ;DPAD_RIGHT
0xd2 108 ;DPAD_DOWN
repeat_key_end
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As I can't seem to find a way to post those here without the spacing being buggered up I've zipped them up here.
Good luck.