12.6V is what a fully charged 3S lipo will be. 4.2V per cell times 3 is 12.6 or (4.2 X 3 = 12.6). I usually use the nominal voltages for these kinds of calculations because it will give you more of an average (although you can calculate it either way as long as you use the same for all calculations). Nominal being the 3.7V per cell or the 11.1V that you're used to seeing.
So the 3S 3500kv will give you on average about 38,850 RPM (11.1 X 3800 = 38,850)
The 2S 4500kv will give you on average about 33,330 RPM. I'm assuming that you're running the 4500kv on 2S because that is the maximum recommend voltage for that motor per the
Users Manual. If you are running it on 3S then you could very likely damage the motor or the ESC eventually.
31/76 gearing will give you a pinion/spur gear ratio of roughly 2.45 (76/31=2.45)
25/76 will give you roughly 3.04
As BG said above the lower your ratio the faster the kit will be. However it also requires more power to turn it as well. This either means more torque is required or it means it will generate more heat. As I pointed out in another post a 4500kv running roughly that same gearing would not get you more than 55-65MPH. i dont care what you LHS or what Traxxas box says. I've been there done that with multiple different motors. Yes if you over gear the piss out of the VXL on 3S with street tires that ballon alot, like Anacondas, you can make the Rusty go somewhere in the 60-68MPH range but you run the risk of blowing out your tires from balloning and you'll heat up that VXL motor very, very fast. The balloning basically increases whats called your "rollout" which also affects your possible top speed. If you're gonna do speed runs with 1/10 scale electronics and you wanna get over the 60+MPH mark without worrying about blowing out your tires while increasing the rollout but not really increasing rotational mass then look at the Jaco foams for the Rustler. There are other things that can come into play like transmission/diff gearing which affect whats called your "overall gear ratio" but I've probably already given you more than enough to process and most of the time transmission/diff gearing isnt soemthing you can change a whole lot anyway.
Now the VXL 3500 is only a 2 pole motor and 4Poles with the same KV rating are gonna give you more torque with the same RPMs. More toque is better for turning those lower gear ratios. However, the higher the KV rated motors will have more RPM per volt but if you have to drop a cell to use it then the advantage is lost and the higher the KV the lower the amount of torque it typically has. Additionally a 550 can will give you more torque than a 540 can so generally speaking your best bet would be a 550 can 4 pole motor thats like double win in the torque department. So when doing speed runs, it becomes this game of finding which motor have the best balance between RPM and torque. Also remember that high KV doesn't mean crap as long as the are sufficient ways of lowering your spur/pinion gear ratio. Most of the time if proper gearing options are available the higher cell count + gearing will usually defeat higher KV. Another way to think of it in terms of doing speed runs would be to find the motor that has the highest KV that will still run on the biggest lipo cell count you want to use and then try and find a 4pole 550 can version of it. For 1/10 scale thats usually gonna be 3S. Although there are a couple out there that will run on 4S. The Castle 2400kv and (supposedly, never tried it) the Tenshock sc401 4000kv. (Btw, as a side note if you go looking for Tenshock motors the 4000kv I mentioned was the older Version1 line. The newer Version 2 line claim to have a 4400kv that will handle up to 4S and a 5000kv that will handle 3S. The Amp draws on these motors are very high for 1/10 scale motors though. anywhere from 180-200A peaks.)
So in this example not only is the 3500 able to push a higher gear ratio its also pushing more RPMs = win. Now I get the impression since both motors are hitting about the same speeds you are running the Viper motor on 3S and basically whats happening is your extra KV is being nullified by the VXLs lower gear ratio. This is why, if memory serves, when you brought a semi related topic up before when you were having problems with your VXL ESC I suggested you get a Castle 1410 3800kv 4 pole or a Tenshock SC401 4000kv 4 pole. Both of these motors have higher KV ratings that the VXL, they are both 4pole and they are both 3S compatible (The Tenshock is also a 550 can motor). Actually according to specs I've seen online at multiple places the SC401 4000kv is supposed to be able to handle up to 18V which means you could theoretically run it on 4S. In order to do that though id say youd want 120A minimum ESC and probably 50+C rated lipos. These are the two best motors I've seen for doing speed runs. I have quite a bit of experience doing speed runs with Rustys using both with 1/10 scale electronics and 1/8 scale.
You should watch my Electric 101 Video series thats stickied in these forums
HERE. It goes over everything thats been said here and much more.