Other Alternatives
You'll note that I asked for the OP's thinking. But taking the points offered:
If you have to buy an engine, you can certainly buy a Ford as inexpensively as a chib.
The small block Ford is smaller and can also be lighter than the chib used.
The SBF has a significantly larger aftermarket than the LS1 chib.
The SBF can be completely independent of any ECU if that's a criterion.
If potential power output was one of the deciding factors, the chib is once more the loser.
Since SCT claim a complete adjustability of operating factors, it would be practical to install any AJ engine. Everything will work, and it's possible to get as much as 500 HP with a factory engine. Used AJ 4.0+ engines are available for less than $3K.
Whinging about ignition coils on engines with 100K miles is sort of silly. We hear about it here because there are many here who want to spend their money on stereo equipment instead of maintenance.
I bought my '02 LS new and haven't had any bad experience with the level of maintenance needed. With 146K miles, I'm on my second set of coils and my third set of plugs. I'm also on my second battery, and I've replaced the alternator. I'm on my third set of brake pads, but still have the original rotors in the back, and I just replaced the front brakes about three weeks ago. I don't have to add oil between changes. So what's to complain about?
KS