i have a LS1 Front cover and LS6 valley cover, can I use them?
no and no.
Will I be able to modify the Automatic harness to work with the t56?
Yes, but which harness are you talking about? The L99 harness or your current LS1/6 harness?
Can you tune the PCM be used?
Which PCM? The L99 or LS1/6? Yes for both, but the LS1 would require extension of the cam, knock, and MAF sensors, add tps and iac, along with a 24x crank reluctor and 1x cam gear swap, or a Ligenfelter converter box. Would also require a DBC throttle body. Or just use the L99 PCM/harness, can convert to DBW.
How hard is it to modify the harness for the swap?
Depends on how good you are at wiring, the resources at your disposal, and ability to read schematics.