Definitely use a Marauder engine. It's already set up for the driver's side intake, and is a newer design anyway.
It will drop right in place on an 03+ panther. The motor mounts are the same. The bell housings use the same bolt pattern (AODE/modular)
The transmission is the actually the same, anyway (4r70w).
Use the Marauder's intake tube and airbox and MAF assembly. It's a direct swap for your TC's airbox but has better flow and an 80mm MAF. You need to drill a hole in the bottom for your stock intake inlet.
You will need to modify the wiring harness a little. You will also need a PCM reflash. Use your stock PCM.
Use the Marauder's exhaust manifolds, EGR supply tube, cats and downpipes, and mount it to your factory exhaust from there. Even better, use the entire Marauder exhaust system with the tips and have the H pipe lengthend 3" for your wheel base.
You may need to use a Marauder brake booster as it's smaller in diameter for more clearance around the DOHC cam covers. Many have been OK with the stock one, though.
If you use your stock torque converter with the new engine, you will need to swap the flexplates as your stock TC is 12". I'd recommend just using the Marauder, or another 4r70w 11.25" TC as then you can use the same flexplate and there is a performance advantage. The higher 'stall' of the 11.25" TC will help you get moving faster.
I think that's most of it. Most stuff will integrate right in place as they are on the same platform. If you're having a shop do the work, be prepared for a hefty bill. Dennis Reinhart has done this conversion on a few panthers before.
Keep in mind, although your top end performance will improve the car will be slower at low rpms. The SOHC makes more torque in the low-end than the DOHC. On a big heavy Town Car, torque is better than top-end IMO. 3.55+ rear gears will almost be a must, otherwise the car will be very sluggish.
IMO, you'd be much better off dropping an Allen Engine Development supercharger on your stock engine than installing a MM engine. You will have more power, more torque and instantaneous throttle response and low end power. The cost would end up being the same or less, anyway.