You need to be careful on this. There is no one set procedure that applies to all experimental aircraft. You have to follow the major change procedure called out in the operating limitations for the specific aircraft you're working on.
The major change procedures have changed and evolved over the years, so what you'll have to do on your aircraft will depend on when the operating limitations were issued.
For many years the limitations simply stated that a major change invalidated the airworthiness certificate! If this is the case for your aircraft, you will need to apply for a recurrent certification. In other words, you'll need to have a new airworthiness certificate issued.
Then there was a time when the operating limitations required you to contact the cognizant FSDO and receive their response IN WRITING before flying the aircraft after incorporating a major change. This would sometimes result in the FSDO wanting to do a recurrent certification on the aircraft, and sometimes it would be pretty routine.
There as a "golden" time from mid 1999 to mid 2003 when the operating limitations issued during that time allowed a major change to be incorporated without any contact with the FAA at all! You were simply required to make a logbook entry describing the change, place the aircraft in a self-imposed 5 hour flight test period, then sign the aircraft out of flight test and back into normal operations at the end of the testing. If you have these operating limitations DO NOT give them up no matter what!! They are like gold and cannot be replaced.
From mid 2003 to present the operating limitations require you to contact the cognizant FSDO for approval of your proposed flight test area for the major change. You must have approval for the flight test area before flying the aircraft after incorporating the major change. The standard test period is still 5 hours, but depending on the change the FSDO might impose a longer test period.
So the bottom line is, check the operating limitations for your aircraft and follow the major change procedure outlined therein. If you don't like the major change procedure you have, you can apply for a new airworthiness certificate and operating limitations. This will not only approve your major change but will also give you the most current version of the operating limitations. This is a recurrent certification of the aircraft and will require an airworthiness inspection by the FAA.
EDIT: Forgot to mention one thing. ANYONE can do the change. You do not have to be the builder, and do not need any sign-off from an A&P or IA.
Hope this helps!