How to burn and rip with CDRWIN
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CDRWIN is THE program for rippping and burning BIN/CUE sets. You can rip and burn other console games with these instructions too. I'll use Ys 3: Wanderers from Ys as an example CD.

How to RIP PC Engine CD games:

First, fire up CDRWIN and put the PC Engine CD game to the drive. Next, go to the "Extract Disc/Track/Sectors" section.

Now you will see the CD Ripping screen.

1. Before you want to rip your CD, decide which kind of rip you want to do. If you want to do a BIN/CUE rip (both data and audio in one big file), then select the "Disc Image/Cuesheet" button. If you want to do a ISO/MP3 rip or just rip specific tracks, then select "Select Tracks" button.

2. Next, select your primary CD reader, or the CD-ROM drive your PC Engine CD is in. You might have to click the "TOC" button to refresh the table of contents of the current CD.

3. Select the filename and where you want to save the BIN and CUE files. Remember to add the suffix .BIN to the filename.

4. Here is the table of contents of the current CD in the selected CD-ROM drive. If you selected to do a BIN/CUE rip, then you don't have to do anything here. If you decided to rip certain tracks or make a ISO/WAV (MP3) set, then you have to select the tracks you want to rip by CLICKING on the tracks you want to rip. 

5. Here you have to select wether or not you want a RAW rip or a cooked rip. If you're going to make a BIN/CUE rip, then make sure that this box is CHECKED. Now the data tracks in the BIN will be in MODE1 2352 (RAW). But if you're planning to do a ISO/WAV (MP3) set, then leave the box UNCHECKED. If the box is unchecked, then the data tracks of the rip will be in MODE1 2048 (cooked). Cooked ISO's are much easier with other programs. However, if you're planning to burn the copy with CDRWIN, then make sure that your burner CAN burn cooked images. CDRWIN is pretty picky when it comes to cooked mode support. You can see if CDRWIN supports cooked burning by going back to the main menu of CDRWIN and selecting "Record Disc". The record disc window has a "Raw Mode" box in the bottom of the window. If the box is GRAYED and RAW is SELECTED, then your burned DOESN'T support cooked burning in CDRWIN. If you can click the box normally, then your burner supports cooked burning. In most of the cases, I recommend to use RAW burning and ripping. EVERY burner on the markert supports RAW. You should only use cooked mode when you rip ISO/MP3 sets.

6. Error recovery. Set this to "Ignore". This way your reader shouldn't stop to the pregap of tracks 1 and 2. This also bypasses Playstation's and Sega Saturn's copy protections, thus allowing the CD to be read. (You will still need a modchip. ^^;)

7. Jitter correction. Set this to "Auto". The jitter correction tries to correct the laser of your reader by trying to read the CD's audio tracks as "sharply" as possible. UNLIKE I SAID BEFORE, this HAS to be either ENABLED or in AUTO! This helps
the gamecoded pregaps to sound perfect!.

8. Subcode analysis. Set this to "Auto". CDRWIN will now automatically calculate the right pregaps for each track.

9. Read retry count. Set this at least to 10. ^^

10. Subcode treshold. Leave this to 300.

11. Skip this if you're making a BIN/CUE rip. If you're making a ISO/MP3 set, you can leave this also to automatic, unless you want the WAV files to be AIFF's instead. You can select the data and audio type here, but I suggest you use the automatic unless you know what you're doing. ^^

12. You might want to save the settings from the "Save Settings" button before starting the process.. this way you don't have to select the raw thingies again. Press the start button when you're ready and then CDRWIN starts the reading process.

13. THE EXTRACTION SPEED. Less speed, less errors. ALWAYS, ALWAYS rip the music track in 1x speed to be sure that the rips WON'T have errors! Since the tracks are read as digital data, then if even ONE byte changes, the track will be corrupted... even though the current CD-R(OM) drives have great error corrections, they aren't perfect... trust me on this.. I've made lots of corrupted tracks when I ripped with full speed.
Data tracks aren't that important, because the drives use a different kind of error correction on those... so you can decide the speed, but to be sure, I still recommend 1x on these too.

IF your burner or cd-rom drive stops to the "Analyzing disc layout" screen, then wait at LEAST 10 minutes. The more tracks, the more time this process will take. CDR drives usually gets past this screen in less than 10 seconds, but DVD drives might crash to this screen... So I recommend to try to rip the cd with both of your CD-ROM drives.
Another thing. Many people have had problems with ORIGINAL PC Engine CD's. They report that the reading of the first audio track stops at 95%. This means that your CD-R(OM) drive CAN'T get past the pregap between tracks 1 and 2. The "Error recovery" at "Ignore" should get past this problem, but if you still can't get past this, then I recommend to set the "Subcode Treshold" to 200. If you still can't rip the CD, then I suggest you try ripping the cd with your other CD-R(OM) drive or then another program, like Fireburner or Instant CD-Wizard.

Now comes one of the most important step.Open the CUE file (it's in the same folder with the BIN) with a text editor, like notepad. Then you'll see INDEX 00 and INDEX 01 commands in the audio tracks. The only tracks which won't have the INDEX 00 command are the audio tracks which are AFTER a data track! Remember, the following is ONLY for PC Engine and PC-FX games.. don't do the following with PSX and Saturn games!
Remove EVERY INDEX 00 command you find! Remember, only audio tracks have them. After you're done, save the CUE.
Example
BEFORE:
TRACK 04 AUDIO
    INDEX 00 06:27:02 <<--- delete this!
    INDEX 01 06:29:02

AFTER:
  TRACK 04 AUDIO
    INDEX 01 06:29:02

If you don't delete those INDEX 00 commands, Fireburner will see the index 00 command as a 2 second pregap! This will show up as totally unsynced audio! CDRWIN doesn't have any problems with this command, so if you use cdrwin, you don't  have to remove them. Anyways, if you remove them, the rip will be 1:1 with the original.. so I almost force you to get rid of them. ;)

How to BURN BIN/CUE and ISO/MP3 rips with CDRWIN:

In the main menu, select "Record disc".

The next window:

1. Click here to load the CUE file of the binary, which you ripped or downloaded from my page. ^^;;;
Before loading the cue, make sure that all the filenames are correct in the cue. After the cuesheet is loaded, you'll see the data of the disc in the screen.

2. Here you can see the index of the disc you're about to burn. You can see that the track number is correct or any other technical details you might want to know.

3. IF you ripped the CD in RAW mode, then make sure that this button is CHECKED! Otherwise the cd will be a coaster. If the ISO/MP3 (or sometimes BIN/CUE sets can be in 2048.. check your CUE file with a text editor.) set you're burning is in cooked 2048, then make sure that this button is UNCHECKED. As you can see from the picture, my burner DOESN'T support cooked burning in CDRWIN.. If you try to burn cooked images and your burner doesn't support them in CDRWIN, then this box is grayed and the program will give you an error. If the button is grayed, make sure that the set you're burning is in RAW 2352.

4. You can make a test burn before burning the cd.. this button burns the cd with the laser disabled, so this is a great option to see that the process goes perfectly. ^^

5. When you're done, press this button and off we go! ^^