Double check the gameinfo.txt located in Steam\steamapps\common\Source SDK Base 2013 Multiplayer\customConfig

"GameInfo"
{
game "customConfig"
title "HAMMER4LIFE"
title2 "HammerLegion"
type multiplayer_only
nomodels 0
nohimodel 1
nocrosshair 1
FileSystem
{
SteamAppId 243750
SearchPaths
{
game+mod customConfig/custom/*
gamebin |gameinfo_path|bin
game "|all_source_engine_paths|hl2/hl2_english.vpk"
game "|all_source_engine_paths|hl2/hl2_pak.vpk"
game "|all_source_engine_paths|hl2/hl2_textures.vpk"
game "|all_source_engine_paths|hl2/hl2_sound_vo_english.vpk"
game "|all_source_engine_paths|hl2/hl2_sound_misc.vpk"
game "|all_source_engine_paths|hl2/hl2_misc.vpk"
game "|all_source_engine_paths|../Counter-Strike Source/cstrike/cstrike_pak.vpk"
game "|all_source_engine_paths|../GarrysMod/garrysmod/garrysmod.vpk"
game "|all_source_engine_paths|../Half-Life 2 Deathmatch/hl2mp/hl2mp_pak.vpk"
game "|all_source_engine_paths|../Half-Life 2/episodic/ep1_pak.vpk"
game "|all_source_engine_paths|episodic/ep1_english.vpk"
game "|all_source_engine_paths|../Half-Life 2/ep2/ep2_pak.vpk"
game "|all_source_engine_paths|ep2/ep2_english.vpk"
game "|all_source_engine_paths|../Half-Life 2/lostcoast/lostcoast_pak.vpk"
game "|all_source_engine_paths|../../sourcemods/*"
game "|all_source_engine_paths|../Team Fortress 2/tf/tf2_misc.vpk"
game "|all_source_engine_paths|../Team Fortress 2/tf/tf2_sound_misc.vpk"
game "|all_source_engine_paths|../Team Fortress 2/tf/tf2_sound_vo_english.vpk"
game "|all_source_engine_paths|../Team Fortress 2/tf/tf2_textures.vpk"
platform |all_source_engine_paths|platform/platform_misc.vpk
mod+mod_write+default_write_path "|gameinfo_path|."
game+game_write hl2mp
platform |all_source_engine_paths|platform
}
}
}

What might be wrong with this that is causing me to only have halflife2_misc models?

Looking at HL2's vpks, hl2_misc is the only one of the vpks that actually contains models.

See if removing the TF2 ones fixes the issue with HL2 ep2 and the episodic content, I want to say TF2 has some content that name conflicts with HL2's.