First, are you getting enough food, sleep? etc. Are you doing the GMs and lunges, but keeping them light? Did you start with accurate or conservative maxes? How often were you squatting and deadlifting before starting Sheiko? What's your conditioning and GPP like? These are all things (and there's more) that would effect how Sheiko would work for you.
The simplest way would be to cut out the second round of the various lifts. This isn't entirely accurate, since while reducing the volume, it increases the average intensity, and one of Sheiko's principles is to have an average intensity of 70% +/- 2%...although on occassion it is lower. I've also heard of doing this, but then taking the top sets of the second round, and doing them after the top sets of the first round...Honestly though this isn't something I've tried, and there's probably better solutions.
Second, #39 has a volume slightly lower, which may work better. There's also the Dave Bates (and no, I don't mean Dave Tate) Sheiko routine...basically it's a 13 week routine for someone who's never done Sheiko like volumes/frequencies, so that they can ease into it. Here's a link:
Sheiko 13 Week Workout
Third, Sheiko allows you to adjust the intensity +/- 5% depending on how you're feeling. So if necessary, reduce the weight. You're also allowed to reduce the number of sets if things feel heavy that day, but you should try and avoid reducing both intensity and number of sets.
Fourth, making use of variations of lifts helps. You don't have to do Sheiko exactly as written, in fact Sheiko himself tells you to "be creative" and that his routines are just examples based on his principles. So if instead of low bar squats all the time, you do some high bar, box squats, pause squats it'll help keep things fresh (just remember to adjust the weights approprately).
Fifth, although this would require some time, effort and math on your part...but you could write a lower volume version yourself. In this post I share much of what I know about Sheiko:
http://www.sherdog.net/forums/44282787-post543.html, So assuming you're good with numbers, know your lifting, and don't mind reading all that, plus read through the portion of Sheiko's book that's translated on EliteFTS (I believe the non translated portion consists mostly of information regarding technique, lift variations, assistance exercises, and sample routines) it's something you could try.
Also, what might also possibly be of interest is this Surovetsky routine:
http://4.bp.blogspot.com/_RUvZfHbKOU8/TKE42pwq9II/AAAAAAAAAAc/iLnj8t7w3bk/s1600/Surovetsky+template.bmp. First, days 1-6 are done over 2 weeks, and second, it'd be good to use conservative maxes...a weight you could hit anytime you went into the gym would be good. You could use Sheiko for bench numbers, look up a Surovetsky bench routine, or something else entirely.
