..and that sounds to be the case in what the OP described.No .. the situation is simple in that the EI should sign off my work and let me collect my money, anything beyond my work is not my problem and is between the EI and the HO.
The only problem seems to be that he did some work in the problem areas, even though he identified to the EI the LIMITS of what he is going to do, so in the inspectable areas now contain parts that are in compliance and parts that aren't. Ex. he put the junctions into boxes in the K&T areas but left the K&T itself as it was. (Again, this is according to my best interpretation what the OP was trying to convey what the situation is.)