That 40A fuse doesn't really "limit" the current to the controller, all it does is blow if current greatly exceeds that for a long enough period of time. Depending on the fuse, it could take a whole lot more than 40A to blow it, pulled for quite a while (at least several seconds, sometimes more than a minute dending on how much overload).
Either way, even 40A is probably a lot more than that motor can handle for long periods. Even if it is a 1000W *constant* motor, and not 1000W *peak* (which is what I suspect is closer to the truth), then even at 48V it would only take 20A constant. Since you have 5 SLA, which at nominal "12V" would only be 60V, but in reality should be more like 68V or more, when fully charged, then only 15A would put you over 1000W.
At 68V, which probably sags to 60-65V under load, maybe further, if it did pull 40A+ becuase of too high a motor load, it could be putting 2400W - 2600W thru the system, most of which is probably turning into heat inside the motor, and the motor is unlikely to be able to handle that kind of heat for very long. My guess is the current is even higher than that, but since the voltage will sag even more because of that, it might still balance out to around that same power level overall.
Exactly how much current or wattage is being used would need to be measured to say how your system is actualy working. I highly recommend a wattmeter, like the Cycle Analyst, Watts Up, Turnigy Watt Meter, or a number of others, but short of that a high-current multimeter or even a 50-100amp analog automotive gauge from Harbor Freight or an auto parts store would at least help you see what current is being used under load.
As for whether 60T or not will work, you'll first need to figure out or measure what the unloaded speed of your motor is at the voltage your system actually runs at, and then do the calculations to make sure the speed you want out of it at the wheel isn't going to be too much for the motor, so the motor can spin at 80% or more of it's unloaded speed when the bike is at it's top speed. This is not a hard and fast rule, but it should help keep you from burning up motors and controllers.
If it is 3000RPM at 60V, it's probably more like 3200RPM at your actual system voltage. 80% of that is about 2600RPM, so you should gear the bike to maintain at least that RPM at the motor when you're at speed, keeping in mind your wheel diameter as well as your wheel chainring size and the motor chainring size.
Personally I suspect you need a much larger wheel chainring than 60T, to keep currents lower in the motor, but without knowing what is actually happening in your system I couldn't say for sure.
Remember--if the motor you are using was rated for 48V at a certain RPM, it's going to be a lot faster at a higher voltage, and you must gear the bike to let it spin as close to that RPM as possible, at the speed the bike will be going at, under the load it will have to handle. You'll also have to keep in mind that the motor will get a lot hotter running it faster at the higher voltage, and it will not be able to handle the full wattage of the higher for as long, unless you can get the load off of it with better gearing.
FWIW, one thing that might help us understand where you are at now, knowledge-wise, and better help you figure out what to do to fix the problems with the bike, is to post some of your final prior brainstorming that led you to what you got for final numbers, that led you to get the parts you got already. Just knowing which parts you got and the results of it only helps a little.
3000rpm motor 60v
24-60 v controller
11 and 44 tooth
12v 12ah total 60v
40amp fuse limiting current to controller
i figure i should be somewhere at 60t sprocket
so all in all i need to get
my1020 48v 1000w motor
about 60t sprocket
and i should be able to ride at lieast 15mph with only 4 batteries so less 9 lbs, and hills come in picture i should just walk it of