Most application portals accept one file. What you have is six — the form, the ID, the marksheet, the certificate.
Merge PDFs →Free every day without an account on some tools. Your file is deleted the moment the job finishes.
The order you choose them in is the order they end up in, which sounds obvious and is the thing most tools get wrong. Pages are copied rather than re-rendered, so the text stays selectable and nothing loses quality.
As many as you need, up to 100 MB in total.
Yes — drag them into the order you want before merging.
Convert the images to PDF first, then merge. It is two steps and both are free.