Im not really a MySQL expert....probably not too many of them around here...thats a question for the MySql specific forums 
As they say "I know you sux, but I sux even more"

As for mysql specific forums 90% of posts there is about "how to connect to the database" or similar type... But if you know of any decent mysql forum drop a link.
As for creating heavy tests, I don't have the budget for that

I need to go with something less time consuming, even if it is not the best solution.
I was thinking, the "Sorting results..." in processlist is probably nor ORDER BY but everything connected to indexes, or to be more precise, it shows up when filesort method is being used (which is called by both WHERE and ORDER BY). What do you think?
Seems I can go two ways:
1) rearrange indexes so no filesort is used.
2) increase buffers sizes (I have some spare memory) (how do you change buffers sizes, anyone did it, is it effective?).
As for my database I have these in red: Handler_read_rnd, Handler_read_rnd_next, Sort_merge_passes, Opened_tables, Table_locks_waited. What is the best method of optimizing these?