I'm new to the Lexus game, can someone tell me what model year had red valve covers? Is it factory and if so, does the red covers signify anything? Any help would be appreciated.

 

Most likely someone painted them. I'm not aware of any that came factory painted, and painting valve covers is pretty common.

It's a pre-VVTi engine, so '97 or earlier.

 

Did you get the ecu with it? looks like a SC harness. You will want an ecu from the same year range as the harness.
There were like 3 different ecu's for that motor before it went vvti. 92-94, 95 and 96-97. I forget the exact split on the 95 year range ones but I think the injector setup changed.