Data says earlier in the movie that the transporter device is a prototype and only has enough power to transport one. As for the shuttlecraft transporters, the shuttlecrafts on the Scimitar were destroyed and damaged from the crashing of the two ships. Perhaps the same thing happened to the Enterprise's shuttlecrafts. Geordi does say that transporters are down. Probably meaning all transporters.
And the idea of of Data overloading his phaser or putting it on a timer wouldn't have really worked. The thaloran radiation was about to be fired at the Enterprise and there would have been no time for him to get back to the hatch he came in from. It was down to something like thirty seconds. Another one of those pesky countdown clocks which always seems to get in the way.