I know this post is a few months old, but I just fixed the same problem with one of my S-RF3 hubs. Mine would clunk in low gear. I could hear it and feel it through the pedals. The clunking hub did it since I got it.

Based on Sturmey Archer's technical information PDF file for the S-RF3, The low gear pawls are HSA 573, pawl for planet cage. The spring for both pawls is the HSA 435 circlip. I compared my good hub with the clunking hub. The pawls were identical, and undamaged, in both hubs. The same goes for the circlip in each hub. I noticed that the pawls on the clunking hub did not spring out as far. They sprang out about 8 mm on the good hub, but only 6.5 mm on the clunking hub. I removed the circlip from each hub, and discovered that the one on the clunking hub was flipped over. The circlip is not completely symmetrical. I flipped it back over to match the good hub and remeasured how far the pawls spring out. Now, the pawls on both hubs spring out 8 mm. This completely solved my clunking problem in low gear.