1) Don't know about Pioneer stand alone players or DVD drives, but I know for a fact (well, 2 Sonys and Playstation2 to be exact) that Sony stand alone players have no problem playing DVD+R media. Regarding media type, I suggest you try a DVD+R instead of a DVD+RW. Chances are the Sony stand alone doesn't like DVD+RW, but that's just my guess as I've never burned on one.
2) Is there any chance you can give PowerDVD a try? After DVD Shrinking the original DVD, use the Open DVD File on Hard Disk Drive function, and select the VIDEO_TS.IFO file.
3) File system was not mentioned in the short guide because I assume the user is using WinXP w/ NTFS format. Yes, definitely convert your file system to NTFS. The biggest advantage is faster system speed (I'm serious), better error correction and management, and a big plus if you encode large files like DVD all the time as it doesn't have a per file limitation like FAT32. You can either convert FAT32 to NTFS from windows (what version are you running anyway? WinXP?), or do a complete reinstall by formating HD, boot with WinXP setup CD and instruct it to convert partition to NTFS format, then install WinXP.