I might be able to help you 
I got it working.
When I looked at my commandline output I noticed doom3 was not looking in the folder, were I had copied the .pks files.
In my home dir are two dhewm folders.
One is hidden, and the path is:
/home/guus/.local/share/dhewm3/base
I got exactly the same error before as you, and as far as I can tell, you’re output is the same as mine. ( so the compiling went right)
Copying the 13 ( might be less if you do not have roe and or the latest updated version,) pks files to that folder worked for me.
I also copied two .cfg files from my previous install to that base folder.
DoomConfig.cfg
default.cfg
Both files contain the same text. ( we probably only need one, but when I was trying to solve the problem, I copied all the text into both files.
The txt in the files:
unbindall
bind "TAB" "_impulse19"
bind "ENTER" "_button2"
bind "ESCAPE" "togglemenu"
bind "SPACE" "_moveup"
bind "/" "_impulse14"
bind "0" "_impulse10"
bind "1" "_impulse0"
bind "2" "_impulse1"
bind "3" "_impulse2"
bind "4" "_impulse3"
bind "5" "_impulse4"
bind "6" "_impulse5"
bind "7" "_impulse6"
bind "8" "_impulse7"
bind "9" "_impulse8"
bind "" "_impulse15"
bind "\" "_mlook"
bind "]" "_impulse14"
bind "a" "_moveleft"
bind "c" "_movedown"
bind "d" "_moveright"
bind "f" "_impulse11"
bind "q" "_impulse9"
bind "r" "_impulse13"
bind "s" "_back"
bind "t" "clientMessageMode"
bind "w" "_forward"
bind "y" "clientMessageMode 1"
bind "z" "_zoom"
bind "BACKSPACE" "clientDropWeapon"
bind "PAUSE" "pause"
bind "UPARROW" "_forward"
bind "DOWNARROW" "_back"
bind "LEFTARROW" "_left"
bind "RIGHTARROW" "_right"
bind "ALT" "_strafe"
bind "CTRL" "_attack"
bind "SHIFT" "_speed"
bind "DEL" "_lookdown"
bind "PGDN" "_lookup"
bind "END" "_impulse18"
bind "F1" "_impulse28"
bind "F2" "_impulse29"
bind "F3" "_impulse17"
bind "F5" "savegame quick"
bind "F6" "_impulse20"
bind "F7" "_impulse22"
bind "F9" "loadgame quick"
bind "F12" "screenshot"
bind "MOUSE1" "_attack"
bind "MOUSE2" "_moveup"
bind "MOUSE3" "_zoom"
bind "MWHEELDOWN" "_impulse14"
bind "MWHEELUP" "_impulse15"
seta com_product_lang_ext "1"
seta sv_punkbuster "0"
seta cl_punkbuster "0"
seta com_videoRam "64"
seta com_showFPS "0"
seta com_purgeAll "0"
seta com_machineSpec "0"
seta com_preloadDemos "0"
seta com_compressDemos "1"
seta m_strafeSmooth "4"
seta m_smooth "1"
seta m_strafeScale "6.25"
seta m_yaw "0.022"
seta m_pitch "0.022"
seta sensitivity "3.301587"
seta in_toggleZoom "0"
seta in_toggleCrouch "0"
seta in_toggleRun "0"
seta in_alwaysRun "0"
seta in_freeLook "1"
seta in_anglespeedkey "1.5"
seta in_pitchspeed "140"
seta in_yawspeed "140"
seta gui_configServerRate "0"
seta com_guid "RbjwWnLrQcc"
seta net_clientDownload "1"
seta net_master4 ""
seta net_master3 ""
seta net_master2 ""
seta net_master1 ""
seta net_clientMaxRate "16000"
seta net_serverMaxClientRate "16000"
seta gui_filter_game "0"
seta gui_filter_idle "0"
seta gui_filter_gameType "0"
seta gui_filter_players "0"
seta gui_filter_password "0"
seta image_downSizeLimit "256"
seta image_ignoreHighQuality "1"
seta image_downSizeBumpLimit "256"
seta image_downSizeSpecularLimit "64"
seta image_downSizeBump "1"
seta image_downSizeSpecular "1"
seta image_useCache "0"
seta image_cacheMegs "20"
seta image_cacheMinK "200"
seta image_usePrecompressedTextures "1"
seta image_useNormalCompression "2"
seta image_useAllFormats "1"
seta image_useCompression "1"
seta image_preload "1"
seta image_roundDown "1"
seta image_forceDownSize "0"
seta image_downSize "1"
seta image_lodbias "0"
seta image_anisotropy "0"
seta image_filter "GL_LINEAR_MIPMAP_LINEAR"
seta r_debugArrowStep "120"
seta r_debugLineWidth "1"
seta r_debugLineDepthTest "0"
seta r_cgFragmentProfile "best"
seta r_cgVertexProfile "best"
seta r_forceLoadImages "0"
seta r_shadows "1"
seta r_skipBump "0"
seta r_skipSpecular "0"
seta r_skipNewAmbient "0"
seta r_renderer "best"
seta r_brightness "1"
seta r_gamma "1"
seta r_swapInterval "0"
seta r_useIndexBuffers "0"
seta r_customHeight "1050"
seta r_customWidth "1680"
seta r_fullscreen "1"
seta r_mode "3"
seta r_multiSamples "0"
seta gui_mediumFontLimit "0.60"
seta gui_smallFontLimit "0.30"
seta s_libOpenAL "openal32.dll"
seta s_numberOfSpeakers "6"
seta s_doorDistanceAdd "150"
seta s_globalFraction "0.8"
seta s_subFraction "0.75"
seta s_playDefaultSound "1"
seta s_volume_dB "-3.809524"
seta s_meterTopTime "2000"
seta s_reverse "0"
seta s_spatializationDecay "2"
seta s_maxSoundsPerShader "1"
seta sys_lang "english"
seta sys_videoRam "0"
seta in_dgamouse "1"
seta in_mouse "1"
seta s_dsp "/dev/dsp"
seta s_driver "best"
seta s_alsa_lib "libasound.so.2"
seta s_alsa_pcm "default"
seta g_decals "1"
seta g_projectileLights "1"
seta g_doubleVision "1"
seta g_muzzleFlash "1"
seta net_clientLagOMeter "1"
seta g_spectatorChat "0"
seta net_serverDlTable ""
seta net_serverDlBaseURL ""
seta net_serverDownload "0"
seta mod_validSkins "skins/characters/player/marine_mp;skins/characters/player/marine_mp_green;skins/characters/player/marine_mp_blue;skins/characters/player/marine_mp_red;skins/characters/player/marine_mp_yellow"
seta g_mapCycle "mapcycle"
seta g_voteFlags "0"
seta g_gameReviewPause "10"
seta g_countDown "10"
seta g_password ""
seta g_showBrass "1"
seta g_showProjectilePct "0"
seta g_showHud "1"
seta g_showPlayerShadow "0"
seta g_showcamerainfo "0"
seta g_healthTakeLimit "25"
seta g_healthTakeAmt "5"
seta g_healthTakeTime "5"
seta g_useDynamicProtection "1"
seta g_armorProtectionMP "0.6"
seta g_armorProtection "0.3"
seta g_damageScale "1"
seta g_nightmare "0"
seta g_bloodEffects "1"
seta r_aspectRatio "2"
seta ui_showGun "1"
seta ui_autoReload "1"
seta ui_autoSwitch "1"
seta ui_team "Red"
seta ui_skin "skins/characters/player/marine_mp"
seta ui_name "Player"
seta si_serverURL ""
seta si_spectators "1"
seta si_usePass "0"
seta si_warmup "0"
seta si_teamDamage "0"
seta si_timeLimit "10"
seta si_fragLimit "10"
seta si_maxPlayers "4"
seta si_map "game/mp/d3dm1"
seta si_gameType "singleplayer"
seta si_name "DOOM Server"
Some lines will be different for you.
The onces important and having to do with screen resolution, full screen, and wide screen are:
seta r_customHeight "1050"
seta r_customWidth "1680"
seta r_fullscreen "1"
seta r_mode "3"
Explanation on what to type in the console or change in the text file:
Tutorial “How to play Doom 3 in widescreen and custom resolutions” - Steam Users’ Forums
If you need more info, don’t hesitate to ask. I am optemistic we can both get it working.