As long as there is a documented trail that the airplane was 51% built by "amateur" builders via pictures and logs, there shouldn't be any problem obtaining the airworthiness certificate.
All maintenance on Amateur-built aircraft is allowed to be performed by the owner or others. The only time a certificate is required (Repairman's certificate specific to the make/model and serial number of the aircraft, or an A&P) is for the condition inspection, which is performed on an annual basis.
Obtaining the Repairman's certificate is a separate process from the airworthiness inspection, although in some geographical areas they can be done at the sime time by the same person. You just have to be able to prove, again via logs and pictures, that you are qualified to do the condition inspection. Sometimes this requires a trip to the FSDO and a discussion with an Inspector to obtain the Repairman's Certificate.
Vic