Should all applicable controls from Annex A to be fully implemented by the time
Answer: Ideal situation would be to implement all the controls marked as applicable in the Statement of Applicability prior to certification audit.
You could leave less significant controls to be implemented after the certification, under the following conditions: (1) to plan their implementation in the Risk treatment plan, and (2) to accept all the residual risks that were not decreased. There is no magic number on the proportion of how many controls must be implemented, and it is in the certification auditor's discretion to raise a non-conformity in su ch cases. Therefore, to be safe you should implement majority of controls prior to certification audit and make sure you implement all the most important ones.
ISO 27001:2013
The process you have set in place seems pretty systematic, but the auditor will look at the results, not the process itself. So for example, the auditor will check if risk owners are nominated for each risk (this is something that is new in 2013 revision), he won't care how you made this transition.
To be honest, I'm not sure how the certification body will react in this case, but basically I agree with your consultant - certification bodies should not issue certificates according to 2005 revision after September 2014. The best course of action here would be to contact your certification body and ask them about their approach.
Minimum of three months for records for certification audit
It is true that ISO 27001 does not require the minimum period of records (i.e. minimum period of the ISMS operation before the certification), however some certification bodies do have such requirements and some don't. Therefore, you should speak to the certification body you have chosen and see what criteria do they have.
You have to assess the impact of risks to confidentiality, integrity and availability of your information - this is part of the risk assessment process. As part of this process you can identify also the assets, but this is not mandatory.
Answer: In section A.12.1 of ISO 27001 you'll find the following objective: "To ensure correct and secure operations of information processing facilities."; further, when you read each control in A.12 you'll see they are very IT oriented.
Question about ISO 27002
You don't have to use ISO 27002. ISO 27002 are only the guidelines that are not mandatory; you only have to comply with what is written in ISO 27001. You'll find a more detailed explanation here: ISO 27001 vs. ISO 27002 https://advisera.com/27001academy/knowledgebase/iso-27001-vs-iso-27002/
Which assets to assess during the risk assessment
If all of these 500 applications are within the ISMS scope, they have to assess all of them. However, if you have similar applications then you do not have to perform risk assessment for each of them separately - you can treat all similar applications as a single asset during the risk assessment process.
Alternatively, you can go for certifications like CISSP and CISM - they are not related to ISO 27001.
2. I am due to go on a foundation course and then the Lead Implementer course and then next year do my Lead Auditors course do you think this is the right way to go?
ISO27001:2013 A.14.1.3 - Protecting application service transactions
It also can apply to financial transactions (between banks, or between an entity with a bank), transactions of database (for example, 2 database that are synchronizing information through Internet), and generally any transaction that involves the interchange of information through a network between 2 applications (think also in a ERP that is connected with an external site where send or receives information).