Eventhough you are following the CL(R&A) Act the licencing authority is the same Factory Inspector. Hence you need to maintain the Leave with wages register and you can produce the records of payment of wages for the earned leave period alongwith the F&F Settlement as followed in other construction sites.
As a principal employer you might have issued the Work Order/Letter of Indent to the contractor. As the strength increased from May please issue the Form V (as per CL Act) and instruct the contractor to obtain the licence. Further you have to give amendment to your RC as adding the contractor name in your RC.
Please try to understand the purpose of any form. Form VI-A is nothing but commencement and completion of contract job to be submitted by the Contractor. If the contractor not obtained any licence then what is the fun of submitting the Form VI-A to the authorities.
For your query No 5 the subject is discussed earlier also. If the contract agreement is for maintenance by the manufacturer then it will be considered as Service and it will not come under CL Act. But if the same is done regularly by the Agency by supplying the manpower for maintenance, then it will be as like contract worker. Further the maintenance team normally comprises 2 or 3 members. So they need not to obtain any licence.
If you have any other doubt please seek.