Fosmids are similar to cosmids but are based on the bacterial F-plasmid. A fosmid library is prepared by extracting the genomic DNA from the target organism and cloning it into the fosmid vector.
you can sequence 40 kbp by NGS (MiSeq reads are 300 bp). Also create degenerative sequencing primer to your target genes from the positive clones. Then amplify they and sequence by a Sanger-sequencer (e.g. ABI 3730XL).
Also you can try Single molecule real time sequencing.
Thanks everyone. I guess the NGS is my best option, as the positive clones came through screening, I don't have degenerate primers for them unfortunately, & Sanger for all this size would be quite expensive.