Will this hurt RFE?
It will be better if you have the grant proposal since they specifically asked for that. But if you really can't have that, ask your boss to state the reason in the letter.
What should be in this letter?
The lettere should be about the grant proposal, how important it is to the national interest, and how important your role is in that grant, i.e. you are the key person and without you, the grant is meaningless therefore the US national interest will suffer tremendously.
How about the statement?
How important the discovery is and how important you are in that project.
Currently I am working in a company as a postdoc. Do I need a letter from the company?
I believe that it is useful. Ask them to write a letter stating why you are recruited to the job is because you are the best one for the position and your GC is important to US national interst, etc.
For the independent letters, should I ask them to write the letters themselves or draft the letters myself and send to them for signature?
You definitely write it yourself and send to them for signature. They don't know how to write a letter like that.
Good luck. Let's hope things will work out for you.