Best Bang for Buck = LC2
I am in the process of putting an LC2 in my 96 Impala SS.
I also have a 65 Malibu SS that I was considering an LC2 swap and I might do it yet.
As far as the best way to go for your money, I can't see any better deal than the LC2.
I just got a low mileage motor, transmission and wiring harness for $1200.
Add maybe $2000 for used turbo, intercooler, injectors, driveshaft, and in a lightweight 65 Malibu you will have a low 11 second car that gets close to 30 mpg.
As far as the engine mounts, you can lower the LC2 (with stock Buick engine mounts) into the Malibu engine compartment (after removing stock malibu mounts), bolt the 2004r in place, line up the trans with the malibu trans cross member or line up the engine so there's enough room between the firewall and engine, and mark the holes that need to be drilled to bolt the buick mounts in place.
If you can't modify the wiring harness yourself, you can get one from Caspers for around $700, but adapting a stock Buick harness to the malibu is not difficult if you read the buick service manual. I was not looking forward to the wiring harness part but it actually is turning out to be the easiest and most educating part of the project. If you figure out the wiring harness yourself, it will be much easier to understand the entire system and diagnose problems in the future.
There is a picture of the green skylark at the GSCA website, I'll try to find it and post a link.
There are actually 2 skylarks with this mod, 1 is blue and 1 is green.