I have taken the configuration of the linksys and I imported in the Cisco.
interesting! the cisco accepted this? how are the ports on the cisco router now configured? what are the mtu sizes?
if the vpn works but SSH/RDP does not then you're looking at an MTU issue in most of the cases. Without config files it is impossible to tell , however.
If you're using UDP mode , try adding
fragment 1000
to see if that helps - you can change the mtu setting on the VPN server but unless you also change the MTU setting of the tap-win32 adapter in windows 2000 itself (using e.g. DRTCP) then the setting is lost. Windows 2000/XP do not allow you to dynamically change the MTU: it's a registry setting + reboot.