missing indexes after system copy

Hi All

we have around 70,000 missing indexes after the system copy

offline export from

source with sun solaris oracle

To 

Linux oracle

but these appeared after we Run  SGEN , which took 60 hours for a 200 Gb database.

and target system response is also slow , how to go ahead with this issue

we have checked export and import logs , none of the packages were missed

1 Why these missing indexes after SGEN , and why SGEN for 60 hours

2  when we check the Tables which appeared in Missing indexes ,from SE14  it says In Consistency with Data dictionary

3  and the other error , is  Index Missing in the database ,

4  but we cant create all these manually.

Regards