Help with PLP Mutagenesis

[Steven_Burghart at BAYLOR.EDU]

     We decided to try this new mutagenesis protocol found in May 95 
Biotechniques.  We got high product concentrations with the first 2 PCRs
(583 bp and 984 bp) but have not been able to get the final blunt end ligated 
PCR product (1576 bases).
     We've tried this about 5 times first using the protocol supplied in the 
Biotechniques paper and then using standard phosporylation & ligation
procedures found in Maniatis before doing the 3rd PCR.
     Any ideas about why this protocol isn't working for us?