Utility Trailer Wood Floor Installation
I strongly suggest that you upgrade to 2x6 (1.5 x 5.5")  The extra quarter inch makes a big difference.

I would suggest using the hex head screws used to fasten down sheet metal roofing.  You can get them in various lengths.  They take a 3/8" socket.

Self tapping screws are fine for sheet metal -- say up to about 18 ga.  I wouldn't want to use them on something like 1/8" steel.

Drill your holes in the frame before putting the planks in place.  This allows you to drill DOWN instead of up, with no risk of getting metal shavings in your eye.  You still will have to put the screws in from the bottom. 

You also may want to put a pair of boards under the motor cycle.  The motor cycle is a point load -- all the weight is on the two tire footprints. This is at most on two planks for each.  

I have a 5x10 trailer with 2x6 running crosswise.  I use it to haul up to a ton of trees, but that's well distributed.  I've noticed a certain springiness on the deck, and would want a stronger deck to use to haul my ATV or compact tractor.