Is there a transaction or Report available to see the scrapped quantity of a particular material where goods issue is done using movement type 551?

If you want to manage the inventory of Scrap, create another material ID for scrap and receive as by-product. When you issue goods against Movement type 551, the material is removed from inventory by writing it off the books.

Is it possible to generate Purchase requisition (PR) with reference to Scheduling Agreement?

PR can be created with reference to another PR and can not be created referencing a PO or Scheduling agreements. PO & Scheduling are created and controlled by purchasing organizations. PR can be created by even end users. For creating PR with reference to another PR, follow the menu path:
Purchasing->Requisition->Create.
Requisition->Copy reference and enter.
However requirement can be generated with reference to Scheduling agreement when MRP is run. For this to happen, source list has to be maintained for that item-vendor combination and the MRP shall be properly set.

How to configure the planning calendar for the ATP calculation where goods are shipped every other working day?

Use Transaction MD25 and define calculation rule for every other working day. Check the lot size settings in OMI4 and maintain relevant data in MMR.

How can we track requisitions that have the deletion indicator set? Can we track the date in which the deletion indicator was set?

You can refer the change document tables cdpos and cdhdr. You can also refer Transaction ME53 under menu path goto-statistics-changes, where the complete audit trails of changes, including deletion are stored.

How can we make a Taxcode as default on purchase order item detail screen

A1: Use condition type NAVS with access sequence 0003 to default the taxcode in the purchase order item using conditions.
A2: Go to IMG.
Materials Management -> Purchasing -> Purchasing order processing ->define screen layout at document level.
Search for the transaction ME21.Double click on ME21. Then search for TaxCode. It is advisable to configure also the info record. The tax code should be a required entry, and whatever you specify here will be the default value in the Purchase order.
Materials Management -> Purchasing -> Purchasing info record -> define screen layout.
When you get here you search for the transaction ME12 ,double click here; search for Input VAT indicator.

How can we delete materials permanently from Material master?

Use transaction MM70 - Material Master->Other->Reorganization->Material->Choose.
Build variant with selection range of material master records to be selected for deletion and maintain run parameters. Execute.
Use transaction MM71 - Material Master-> other-> Reorganization->Material->Reorganization
Build a second variant
Maintain run parameters and execute.
It is also important to remove the records manually from info record, POs, PRs, reservation etc for successful deletion of the material.

How can I use variable size items?

For example, consider an item A with 'kg' as base Unit Of Measurement(UOM) and 'm3' as stock keeping/issue unit. Conversion factor is 1kg = 2.4 m3.
In the BOM of 'B' ,number of A required are specified (say 5).
Specify the 3 variable dimensions i.e. length, width & thickness- say 2000mm X 3000mm X 4mm = 0.024 m3
As per BOM - 'B' , the quantity of A required is 0.024 X 5 = 0.120 m3
If a production Order is released for 15 numbers of 'B' , the quantity of variable size unit will be 1.20 m3.
You can change the length, width or thickness in the production order & check the resulting variable size item quantity. At the same time this requirement can be seen in 'kg' in stock/requirement list.

How can I extend all material to a new plant?

The SAP program - RMDATIND is used to create /update material master record.

Can we have more than 6 standard values in standard value key?

One way to achieve this is to create another operation step using the same work center. However this shall be with a control key that is not a milestone. When the milestone operation is confirmed, the previous operations up to the next milestone are automatically confirmed. To get the desired number of standard values , all the 'non milestone' steps can be built depending on the need.