So here's some examples of the problems I ran into. I bought truck coil packs with the mistaken understanding they would work for my application. Technically, the coils would work, and some builders say the truck coil packs are slightly superior because of higher heat tolerance. However, they most certainly can not be mounted in conjunction with the F/Y body fuel rails. See below. Note how the fuel rail connection points directly into the coil pack connector. I guess guys who use the truck packs must be using after market fuel rails.
Next, note the rather substantial difference between F and Y body balancers. The Y body on the left is much tighter to the block. I recommend the F body because it gives a little more clearance away from the block, which will come in handy for mounting an R4 A/C compressor in front of the passenger side head. You cannot use the stock A/C compressor because it completey interferes with C3 control arms.
Other gotchas.
The LS1 intake from a Y body does not have the threaded inserts to mount the throttle cable bracket, which is necessarry for our C3s . . . unless you want to try and get a fly by wire setup to work. This is not such a huge problem since I'll take the opportunity to upgrade to an LS6 intake. Note, there is NO smog legal intake other than stock in CA. BBK is working on getting an E.O.#, but they don't yet have one.
The TPIS headers I got with the motor came from a Y body as well. Regrettably they tie together underneath the bellhousing area and go straight back. On the Y body, there is space because there is much more clearance by the torque tube as the transmission is in the rear. On my F body like setup, the bell housing is much larger as the transmission is in the front and therefore no room.
Finally, the motor as of a few days ago:
