According to me, I guess you have to re-apply your VISA and then wait for your Visa and then apply for a single entry visa. But if you want to re-apply then the best way is if you do eVAL which will come within 48hours I guess.
You are required to obtain an offer from Al-Madinah International University first. Once you have received the offer, you need to liaise with City University to cancel the current VAL.
Since you have not obtained a Student Pass, you are required to exit Malaysia and reapply for the VAL. The processing fee for the new application is applicable. There is no guarantee that you will be issued with a new VAL under the new institution, as the approval is solely at the discretion of the Immigration Department.