Much like the cooling system, if you are retaining the same series of engine in you car then motor mounts won't pose any issues. If you are changing from old school to LS then you are going to need new mounts.
Doug's headers offers a conversion plate that is made out of laser cut steel and allows you to bolt on a conventional small-block motor mount to the side of the LS. Fesler Billet has a different option in the way of an eye pleasing billet motor mount. These engine mounts require a bracket to be fabricated that goes from the motor mount to the crossmember, but they will look great once installed.
While most of the engines shown have exhaust already, some do not. Like we have said numerous times, if you are staying with the same series then you may not need to change your exhaust system. There are specific swap headers out there like these from Doug's Headers that are specifically designed to mate up to a LS1 or LS6 stuffed in a '64-72 Chevelle. Doug's also has them for '67-69 Camaro and '68-74 Novas. These headers will provide more flow over stock manifolds and really let that new LS breathe.
If you decide that your ride just has to have a six-speed automatic like GM's 6L80/6L90 then Mast Motorsports has a controller set up you need. Mast's M-90 drive by wire ECM is a propriety marine grade controller that is fully laptop programmable via Mast windows based tuning software. So, whether you have a column shifter or floor shifter in your vehicle, you can run the new GM 6-speed auto. Since the ECM has GM's LAN embedded, you can fully control the functions of the GM 6L80/6L90 transmissions.