Welcome to the site! Lots of good people and info here. Nice looking Malibu! Looks and sounds like you've made a good start on it already. What brand of parts did you use to do your LS conversion?
The parts that I used for this LS conversion are as follows:
Engine - a 2004 LS 5.3L Cast Iron Block, Comps Cam and Bee Hive Springs
Transmission - 2004 4L60e rebuilt to 4L65e specs. G Force crossmember. The stock GM TR Sensor on the side of transmission provides P & N Safety switch plus back light control. I used the Holley Front Accessory Drive System, Corvette water pump and harmonic balance. I used the Holley oil pan and the fit is perfect!
Throttle is Drive by Wire (truck pedal and TAC module). Rather than modify a GM LS wiring harness, I bit the bullet and purchased a Painless Harness. The ECM is a Blue Green 411 model. I have a friend who has HP Tuner on his laptop and he did the re-programming of the ECM.
I kept the stock clam shell motor mounts and used Dirty Dingo sliding motor mount plates. I also am using the Dirty Dingo mounting bracket for the ECM. For exhaust, I skipped using headers and instead used the GM LS3 crate motor cast manifolds. The passenger side manifold dumps very close to the frame, so I may have to do some slight modifications. On the driver's side I will be getting rid of the stock brake master cylinder and proportioning valve and replace it with a Wilwood setup. The aluminum radiator is from Northern Radiator as well as the dual electric fan shroud. The car did not have factory AC so I am going to leave it as is.
My next challenge - replace the stock 7.5" non-posi diff and 2.29:1 gears. I am searching for a set of 3:42 gears and a posi.
Hope I have answered your question - thanks for your words of encouragement too!