SOPC to Qsys Migration , fitter issues , pin count increased by 300%

HI I had old Sopc based setup and after few modification I have ported it to qsys ( i.e. changed the Ethernet IP name in old .sopc manually) , everything got compiled successfully but in fitting 928 pinout cant fit into 328 I/O's ? please let me know what could be the issue ? however everything got upgraded from Quarts 9.0 to Quarts 13.1 Cyclone III was the device in both cases.

waiting for suggestion ?

changed I did in migration

PLL - Removed ATPLL - Added

triple_speed_Ethernet - Updated

DDR2 Burst changed 4 to 8

used *_tw.tcl files to add some old IP Stuff AvalonReadIO (custom group of IPs)

Waiting for response, I am stuck in this situation from long back :(