I have replaced Philips screws here and there with Allen or Torx. The ones that matter to me are the four on the bottom of the float bowl, so I can pull it off and get to the jets in moments. Also, the studs on the exhaust where it couples to the head, the one in the muffler (up the little hole underneath)and the three bolts that hold the stator on to the flywheel. Most or all of these were replaced because they refused to come with standard methods, and the exhaust had to be drilled and re-tapped. In addition, I replaced the fuse holder with one that takes 15-amp mini blade- type fuses like my van when I found out it took Yamaha, not buss type. When my flasher relay went out, I found that Yamaha wanted thirty bucks for their rectangular one; discount auto usa had a universal round one with the same three prongs for $2.99, which meant I had to tape up a holder out of site where the other had been. It is a Tridon 552, DOT should it matter. I also have two thrust washers in my kick starter to reduce shaft end play.
Two items from the old forum I appreciate and don't know who to credit-- a 3/4" copper street 45 over the end of the tail pipe, and the extension groove on the high beam switch that shuts off the headlight for all those times the other guy isn't there to need it.
I estimate all of the above cost about what the OEM relay would have. GB