TIER2 EXTENDED VISA - REFUSED(Job Skills Unsatisfactory)

[Sals2189]

Hello,

I have been working with a scientific company for the last 3 years with an approved Tier 2 visa. My visa runs out end of March,2017. I applied for Tier 2 extension visa, one month prior to deadline using 10 day priority postal service. I received a letter saying the visa has been refused due to unsatisfactory job skills. I got full points on all other aspects of my application including right salary.

My employer had used the same job description - job code as used 3 years ago during 1st Tier 2 application. Although since then, I have been promoted to higher level role in the company and with more responsibilities. However, my employer and I thought it would be best to not change the job role/job skills at this stage as the employer would have to re advertise for this new position etc. So, we kept the same job details as used 3 years ago. The home office said, my job skills required for such type of job was under qualified and the job was meant to be for a higher personal with a PhD degree etc. I do not have a PhD degree because I did not need one for this particular job role. Now my employer needs to go back and understand the different job codes/job types and skills required.
Questions for help
1) How do I reapply for the extended visa?
2) How does my employer justify that they got the JOB CODE wrong and that my skills are MORE THAN sufficient for this type of job.
3) What happens if i pass my expiry date for tier 2 visa. How much time do i have left to re-apply?
4) What else can my employer do to appeal to the UKBA to justify my job skills = job code are correct ?