Had the same problem. 2-3-4 gear acceleration under load clunk from transmission engine side. sounds like the valve tap the piston or lose bolt in engine bay or something in transmission. SOLVED after replaced the fly wheel. 2010 Mazda Speed3 6speed. if you dont have timing problem. I replaced the OEM flywheel but i think is better to go with aftermarket you will never have this problem again.
2010 Mazdaspeed 3