SbassLaser

Sounds like theyre trying to upsell you on equipment thats not needed. An isolator is typically used to prevent parasitic draw or for running your system with the car turned off so it keeps your main battery charged. If youre using two batteries with similar resting voltage, which they should be since they are both lead batteries, an isolator is not necessary. Ive never heard of someone needing a regulator or charger for a second battery. Just wire the two batteries in parallel and send it. Like chevyboy said it would be best if they were both AGM but having one AGM and one flooded cell shouldnt cause any problems. Overcharging would only be a concern if your charge voltage is too high, the current draw will drop to near zero when the battery reaches a full charge.

For the port size and length you should model the enclosure in a program like winisd that will show you the port air velocity and excursion so you can see how different sizes of port will effect how it all performs. You don't need anything to direct the airflow to the ports except for a flared end piece. Keep the end of the port away from the back wall by at least the diameter of the port. I.E. a 4 inch diameter port should have at least 4 inches clearance at the end of the port.

Did you ever build either of these designs? If so, how did they turn out?