OSI Model – What Layer Deals with Ports?

Your question is really too broad, and home networking and consumer-grade devices are explicitly off-topic here, but I will try to give you some general answers.

1. PPP is a layer-2 protocol, the same way that ethernet, HDLC, frame relay, ATM, etc. are. PPP is specifically a point-to-point protocol with only two endpoints. Other protocols, e.g. ethernet, are designed to work with multiple possible endpoints. Because ethernet, and other IEEE LAN protocols can have multiple connection, they use MAC addresses, but PPP doesn't.
2. I don't really understand your second question. PPP is a layer-2 protocol, but IP is a layer-3 protocol. In general, layer-2 protocols don't care about layer-3, and they can carry any number of layer-3 protocols.
3. Ethernet is both a layer-1 and a layer-2 protocol. PPPoE uses PPP for the layer-2 protocol on an ethernet layer-1. The PPP frames are encapsulated in ethernet frames. As far as your traffic is concerned, it is passing through an interface that uses PPP as the layer-2 protocol. PPP can be used on multiple different layer-1 interfaces, e.g. serial, ATM, etc. PPP adds some feature that allow you to negotiate layer-3 addressing, data compression, authentication, etc. that do not exist in other layer-2 protocols.
4. Your fourth question doesn't really make much sense. You seem to be comparing apples to oranges. PPP is a layer-2 protocol, but PPTP basically allows you to extend a LAN on top of other protocols. As you wrote, it is above layer-4, and the layer-2 protocol used when using PPTP could be PPP. Unfortunately protocols above layer-4 are explicitly off-topic here.
5. PPP frames are not wrapped in IP packets. It is the other way around; IP packets can be wrapped in PPP (or other layer-2 protocol) frames. Neither layer-2 nor layer-3 know anything about ports, which are layer-4 addresses for some layer-4 protocols. Routers strip off layer-2 frames from the layer-3 packets, so the router on the other end of the PPP link will strip off the PPP frame. A router will then route the layer-3 packet, and it will create a new frame for the new interface for the packet. By the time the packet gets to a server, the PPP frame will be long gone. The server will have a network stack through which the frame it receives passes. When it gets to TCP at layer-4, then it will have the port used, and it will know to which process in the server it should send the TCP segment.

That depends on the physical layer - there's a multitude out there - and your point of view.

For example, Ethernet adds a preamble/syncword combination to a layer 2 frame, providing bit and word synchronization. Some might call that a "header". The L1 PDU is the Ethernet packet, the SDU the frame.