Apologies for taking a while to reply: I had to check on a few things. Some answers:
"stemlength" is clearly described in the RAINFOR-GEM manual section 1.5 where I put a photo I took of a tree at Wayqecha: it is the length from the base to point A (not B or C) on that photo.
How to calculate aboveground NPP: this is not described in the manual, but briefly described either in Yadvinder's 2009 paper http://www.geog.ox.ac.uk/~ymalhi/publications/Publications2009/2009-gcb-comp-assess-of-carbon-product.pdf or in the Plant Ecology & Diversity papers coming out just now (which I'm sure will be posted on GEM within a week or two).
I am actually working on another paper just now describing these calculations in detail and how exactly to account for branch turnover and other terms (leading on from the Plant Ecology & Diversity papers). This paper isn't finished yet but I should have it complete before the Pisac meeting.
If you will be at Pisac next month perhaps we can talk about this some more?