If the LS 1 & 2 Thermostat Housing style works better for you (often the case in LS configurations), it is possible to modify the housing plate to fit the LS 3 pump.
To make it fit, elongate the existing countersunk holes to reach the 3.070" bolt spacing. You can then use a washer and longer bolt to secure the housing to the pump.
This modification is done frequently in LS setups with great success.