Can an incorrect fuse (20 instead of 15) cause the transmission to run badly? Now that i've replaced it with the correct one it seems to be running better-not straining in second gear.

 

Good its running smoother, but fuse is not to thank. Only difference is the current at which they blow. You didn't say anything about blowing fuses. Fuses are sized to protect wiring and components from burning up and torching your truck. Flaming wire harness + truck = bad.