The factories worked normally until today when all types of factories suddenly just stopped working.

No idea what things to suggest as 1.6.4 is a very old version, and I am not even remotely familliar with the code due to only having joined the dev team last year. I also am not sure what you mean by "stopped" working but unless something worked very differently back in 1.6.4 none of those inputs are valid recipes in the combiner. I believe you need 8 of one type of dust to combine with the stored cobblestone to create a gold ore.