Bigmike brought up a point I hadn't considered but one that just affected me the other day. Some efi setups can have enought juice to turn over but not enought to easily start. I just went to my storage unit the other day and attempted to start my bike, the fuel pump sounded fine when I turned the key on but it turned over slowly and didn't wanna start after a few seconds, turned it off and tried again and it didn't have enough juice left to crank over. I charged up the battery and it worked fine again. The most important thing to check with your battery is how well it load tests, even if it charges up to 13 volts it might load test down to 9 and be worthless. Before too much more speculation you should give us more details, is it turning over slowly or normally, does it seem to have resisitance or almost free spin? You don't have a lot of compression already, but if your engine is getting pretty tired you might not have enough compression to cause proper ignition. Good luck and keep us posted.
