Basically there's:

1) Legal fees for SPA
2) Stamp duty upon MOT/DOA
3) Legal fees for loan documentation
4) Stamp duty on principal security documentation

Although 3 and 4 are included in the loan, you still need to pay for 1 and 2.

Standard procedure is to pay during the execution of the SPA.

However, it is between the client and the lawyer. If the lawyer agrees to grant you an extension of time to pay the fees, then all is good. There's no hard and fast rule although in most cases, when the purchaser is the client, the lawyer would demand for fees to be paid upfront. If vendor, there is still the opportunity to deduct it from the balance purchase price.

So do talk it up with the lawyer.

Small matter. Just go to the nearest LHDN office with a certified true copy of the stamped SPA and request for a new Nombor Rujukan Cukai. They will immediately issue you both with respective numbers. Free of charge.

Don't have to worry about being taxed for it. It's just for their reference. 

There are no stupid questions bro 
Four copies will be sent for stamping - all four are identical as to contents - one will then be marked with a chop as ORIGINAL while the other three will be marked as DUPLICATE.

So, the blank part which you are referring to would be in all copies, not just your duplicate.

With regard to EPF, they would mostly just check on the purchase price, property particulars, the parties to the agreement and cross-refer with the letter of offer from your bank to see if the details match. I doubt if they will make an issue out of the omission. Keep your fingers crossed they don't notice it. 
If you're taking a bank loan, then the bank will retain the original until the loan has been subsequently redeemed wherein all original documents will be returned to you. In the interim, you can keep the duplicate which is duly stamped and has full effect in law.

When there's no title, Deed of Assignment (DOA) is the document which proves transfer to beneficial ownership of the property from the vendor to you.

Are you sure that they require the DOA? Unless you're buying by way of cash? From what I understand, they require the SPA, letter of confirmation from the developer and letter of offer from your bank as supporting documents.

* am assuming that this is a subsale and you're taking a loan.

http://www.kwsp.gov.my/index.php?hdl=bin&rp=1286