The procedure now is :-
1. submit application for 'change of engine' to JPJ putrajaya the kawal selia, techincal department, with all valid document (i.e. reg card, application form, invoice of engine purchase, custom letter, I.C....). all documents need a photocopy.
2. after u submit, u'll get an acknowledgement slip, which has a reference number & phone number u can call to check the status of application. Normally the approval duration would be 2~3 weeks. Mine took 3 weeks.
4. Call in to check after 2 weeks, if approved & readied. Go back to JPJ putrajaya to show them the acknowledgement slip and take the approval letter, check all particulars b4 leaving the counter to ensure all details are correct.
5. With that approval letter, go to puspakom and inspect your car. During inspection they will check the chasis number, engine number, windows got tint or not, brakes condition, suspensions condition, exhaust emission and smoke.
6. if all the above are in good condition, then Puspakom will LULUS ur inspection.
7. After puspakom LULUS the inspection, u need to endorse your insurance too!... some insurance charge
minimum of RM5~Rm15 for the process. Then, take the puspakom 'report card' with other documents (reg. card, custom letters, invoice, jpj application form, insurance endorsement to endorse change of reg card's particulars) to JPJ (can do at branch, not necessary must be JPJ HQ @ putrajaya) to submit for endorsement of change of engine number along with any other particulars that u need to change on the reg card (i.e. colours?? transmissions type???)
8. Then depend on which JPJ branch, some will give u another slip and ask u collect the amended reg card a week later or 2 weeks later, or some jpj branch (i heard) can gau-dim within just few hours of waiting.
From my experience, the most important thing is the first approval letter from JPJ.
if for 1.3-> 2.0 and the first approval letter form JPJ kawal selia technical department ALREADY APPROVED, then puspakom have no say in anything (except u mod engine mounting, they can fail u on that), and puspakom will just inspect the rest (brakes, suspensions, engine & chasis numbers, ENGINE MOUNTINGS). and normally puspakom will not ask/tel u that 'oh 1.3 -> 2.0 cannot la.' those craps, cos if their responsiblity is just do inspection,... only JPJ has the say of the 'do's and don'ts'.
above is jst 2 cents from what i know. any wrongs, pls correct me..
thanks.
p/s: I did the jpj applications and puspakom inspection myself in Nov-Dec 2006, the only fees i paid is the puspakom inspection fees which is Rm40.. or isit RM45 (i can't remember), But time consuming a bit, as need to go here go there myself. mine engine transplant was 1.6->1.6 ... hehehe.. :D