So under Section 5(5) the Branch Manager would be the "deemed CPIO" for having received the RTI Application in original and not transferring it under Section 6(3). There have been several CIC / SIC decisions to this effect.
So Kaushal, you have to decide on your priorities. If the information requested is urgent, go in for a fresh RTI as recommended by Col Kurup. Else file the 2nd Appeal, pointing out all the errors and omissions discussed in this thread.
Re: How yo file complaint aginst CAPIO for not follow the procedure of the act and giving incomplete, false and misleading information.
The replies from the CAPIO has absolutely no legal standing from the RTI point of view. If the reply furnished by a CAPIO satisfy your requirement and it is signed by a Gazetted Officer, it is not worth persuing as your requirement is fulfilled. In case you are not satisfied with the reply, things are differant. In your case the case is barred by limitation for FirstAppeal. To me, it will be better to make a fresh application without giving any reference of your previous one and changing the wordings a little bit to give the appearance that it is not the same old application.