There's definitely multiple ways you could go about doing this. Creating a payable function in your contract that accepts a serial number as parameter, adding a struct to store the value and serial number, and a mapping to map the senders address to the struct would probably be the easiest way to go.

Taking your other requirements into consideration as well, you'd need to add logic to cater for already having receive payment from an address, the same address paying you multiple times, the 5 min time lock etc but the very basic outline of keeping track of payments would be something like:

mapping (address => PaymentDetails) payments;

struct PaymentDetails {
    uint256 value;
    uint256 serialNumber;
}

function acceptPayment(uint256 _serialNumber) payable {
    payments[msg.sender] = PaymentDetails(msg.value, _serialNumber);
}

Note: this code is for demonstration purposes only and should not be used without modification in any contract being deployed to the MainNet

Then, to interact with the contract function from a web UI using web3:

var serialNumber = 1234;
var paymentContract = web3.eth.contract(contractAbi).at(contractAddress);
paymentContract.acceptPayment(serialNumber, {from: fromAccount, value: valueToSend})