Don't put the transports behind the walls, and if you aren't using the factory guard reserve, pull them out of the main base, too. You're wasting a lot of shielded real estate on big junk buildings.
Next, get the shields back. You want them behind the walls, or they are easy pickings. Burst turrets won't work well lined up like that behind the walls. At level 7, hailfires will easily pick them off. I recommend staggering them in a zig zag pattern with collectors in front of them. You can check my base to see what I mean (Boogie in crimson_ALLIANCE). I switched to bursts several months ago, and my base works pretty well, especially with the latest increase in turret equipment buffs and just the burst turret damage. Some (not all) hailfires get into turret range when they are forced to go around buildings to get at their nearest target, so a big hfd attack is not necessarily a death blow to the base.