This is a very good amp, well worth the effort of repairing it. I went through my share of Marantzes, Denons, Sansuis, NADs and many more, and this amp is now in my main rig. I don't think it will be replaced anytime soon.
Once you have it fixed and get to adjustments, note that they should be done with 8 ohm load connected (I just used an 8 ohm speaker) and amp running with no signal for 10 minutes before the adjustments.
I did idle current first. It was more than double the value in the service manual, and the amp was running quite hot. I used transistor legs as measurement points. Not easy, but I could reach them with multimeter leads ending with pins. You connect the multimeter to the source (right leg) of Q114 (black transistor on the outer right) and source (right leg) of Q116 (green transistor on the outer left), measure and adjust for 17 mv. Then connect multimeter to sources (right legs) of the inner black and green transistors Q113 and Q115 and measure. If it's between 15 and 20 mV, OK, if not, readjust so that both measurements are in that range. They were not the same in my amp.
It helps if you have someone to help, much easier to do this with 3 hands.
I adjusted DC offset using hot (+) speaker terminals for each channel as + measurement points and chassis as ground, with 8 ohm speaker connected. Note that the SM refers to "speaker terminal 6/8" not "checkpoint 6/8" or "P6/P8". The points marked P6, P8 on the power amp boards are for something else, no clue what.
There's a third trimmer on some versions of the power amp board (including mine). See here:
http://www.audiokarma.org/forums/showthread.php?t=579212
I did use it to adjust DC offset (actually had to use it, I could not get it down to near 0 mV using VR101), but I have no idea if it's its intended purpose.
EDIT: I did a quick search and if your outputs are blown, you might have a problem. 2SK343 and 2SJ99 are not easy to find, and quite expensive. The only source I'm finding for Hitachi originals is a seller on the auction site, with prices around $20 for 2SJ99 and $30 for 2SK343. If you need to replace all 4, that would be $100, quite a lot to repair this amp. There are parts with the same model number on alibaba (cheap), but I'm not sure if it's the same part, possibly something else with that number. 2SK344 and 2SJ100 are possible replacements, but those could be even harder to get. You might want to look for another S-6040CP (or its Inkel/LXI counterpart) with a blown channel and use it for parts.