Hello Bharath

I would try to answer a few questions for you, but it would be better to have some of the questions asked again (in another thread with the tags RQM and DOORS)

1. Yes you can migrate CLM 4.0.1 to CLM 4.0.3 M4.
But please note that Milestone (M1, M2, M3...Release Candidates (RC0,RC1, RC2..) are not final THE versions released by our developement. These are  early spins, which you could setup for Beta testing. Issues arising out of this build - are not eligible for regular support. So please do not upgrade your production setups.

2. While upgrading its mandatory for the JTS to be on the highest version. Although its preffered to upgrade all the related applications to the same level as the JTS, but you need to first upgrade JTS.

3. I wish there was Question :)

4. Not sure.. But the integrations with DOORS connect to the application directly not JTS.
**I am going by how RTC-DOORS integration is setup.

5. I am not sure if Data exchange is the right word to be used. The OSLC based integration allows you real time access to the RQM resource from the RTC resource (its like a real time query to the related resource). This happens between the 2 applications.

6. Yes, RQM and RTC communicate/integrate using OSLC.

+ what Krishnakanth mentioned, if you keep application at different versions, integration features may not work as documented in the higher versions.
Looking at the last 3 questions it feels like you want to know more on how the different applications communicate in Jazz platform. You may consider reading about the Jazz Integration Architecture in the link below
https://jazz.net/products/DevelopmentItem.jsp?href=content/project/plans/jia-overview/index.html