jDoom is one of the components supported by the Doomsday Engine (others are JHexen and JHeretic). This is definitely the best Doom source port I've ever seen because of its support hi-res textures, 3d models, lightning effects and other effects.
Unpack your Doom files to the separated folder (this was 'D:\games\doom' in my example)
Download project installer file and start installation. The setup procedure is pretty standard and simple. There is no need to install the Doomsday Engine to the Doom's folder, because the single installation of this engine can be separately used for many Doom's, Heretic or Hexen versions and addons. So, just leave an installation path set by default.
After the end of installation, start Doomsday Engine from Start Menu. A Setup Wizard will appear and you will be prompted for the default Language. Select your language and click next.
Select a game profile you want to use. In my case, this was an 'Ultimate Doom'.
Click '....' (Browse) and point the path to the WAD file of the game you want to use. WAD file is a standard Doom engine's resource file, containing textures, sounds and maps. It's usually located in the same folder where you have unpacked your original Doom files in step 1.
You can skip the Addons screen by clicking 'Next', if you don't want to use any addons.
Doomsday Engine Frontend will appear. 'Shared Settings' is a set of optins that will be used for all game profiles and types, that are supported by Doomsday, unless you set up some settings separately, so the 'Shared Settings' is what we most likely want to use here.
Open 'Shared Settings'->'Settings' tab->'Display' option. Adjust your screen settings according to your hardware capabilities. You can try to change a 'Renderer Library' to 'Direct3D' in case any in-game rendering problems appear on your hardware.
Open 'Shared Settings'->'Settings' tab->'Graphics' option. Ensure that 'Anisotropic Filtering' is turned on for a sharper in-game picture.
Select your game profile on the left side of Frontend ('Ultimate Doom' in my case) and click 'Play' to start the game itself.
Adjust keyboard settings in 'Options'->'Controls'.
Turn on 'Mouse Look' and adjust mouse sensivity in 'Options'->'Mouse Options'.
Open 'Control Panel'->'Video' from 'Options'. Adjust 'Gamma', 'Contrast' and 'Brightness' settings.
Ensure to turn on '3D Sound', '16 Bit Sound' and '44100 Hz' sample rate in 'Control Panel'->'Audio'.
Open 'Control Panel'->'Graphics' and turn on 'Always render full sky', because you will surely need this feature in some Doom maps.