Out of all of those PCI-E o/c makes the largest difference.
Of course going too far is going to hurt, sometimes badly. (your data, silent corruption, etc.)
I'd keep it under 110, some hosts, notably the Areca 1880ix series, have a hard shut off at approximately 108MHz. Go 109 and the BIOS is skipped on POST!
I had 1680 and 1280 controllers that would go as high as 115 but 1bit ECC trips were fairly common on i/o intense tasks. I would NEVER advocate such a high PCI-E o/c on production hardware. (I always twist arms until something gives just to see what actual limits are, however.)