Uncontrolled throttle response

2003 Honda what? With which engine and transmission?

Well actually i was working Crown (Chinese Company) 70 CC motor bike engine with gear box attached to it. I am using it because ignition can be installed on it. Engine is fixed over test rig.

Okay, that sounds like an interesting project. From your description it sounds like the injector flow rate is higher than required for this application. It flows so much extra fuel that it is like you are at full throttle. You need the flow rate of a tiny perfume dispenser but the current injector is a garden hose.

What did the EFI unit come off of? I suspect you will need to lower the fuel pressure or find a lower flow rate injector, or find someone who can remap the current ECM to work with that engine or more likely a combination of the three. Lower pressure will reduce flow but the lower pressure will not atomize properly.

You could also look at the resistance of the current TPS between 0% and say 5% and see if you can stretch that out using a different resistor.

My TPS is working fine and it is providing right values of butterfly position it is giving me 0% reading when fully closed and 100% when i press full throttle, these readings my software provides me so i do not think that there would be any problem with resistance of TPS what say? Also it is important to mention here that I am using speed-density method for tuning (which reads MAP sensor reading),since i want to run engine on low RPM about 5000-6000.

What did the EFI system come off of? I've never seen a fuel injected engine under 200CC or so and those are on a lawn tractor.
From your description the entire system is able to flow far more fuel that the engine can use. That means you need to figure out a way to make it flow less fuel.

Well EFI kit i am using is a general kit for small engines from 50 CC to 350 CC. Kindly please remove my one confusion according to my little knowledge high fuel flow would increase the AFR value but RPM would not be that much effected however increasing air flow would increase RPM thats what we do when we pedal the accelerator. Can it be a problem of a big throttle body??

That is a huge range for one kit to cover. Air+ fuel increase rpm. Ideally you want the throttle to be around 75% at the engines torque peak. I would say the throttle body and injectors are both larger than needed. Does the maker of the kit have a support line? They might be able to point you to a particular setting or programming curve to use for the smaller engines.