If everything is in order, the only thing to hit when you bottom out will be the bump stops on the frame above the rear axle. Usually replacement exhaust pipes don't go high enough over the axle and almost always will be hit by the rearend, and I'd bet this is what you are hearing.
The soft springing is common on the goats, and we all have to do some work to carry people in the rear seat - not to mention that the cars were lower in the back than the front even when new.
If you only needed the rear up about an inch, there's an easy solution. You just get a large 3" washer and bolt it to the top of the center portion of the spring mount, and use a 2" by 1/2" bushing on top of the washer so the spring won't slip off the washer. Run a Grade-8 bolt through the new assembly through the hole and back it up with a 1.5" washer on the bottom and you're set to go. Tough to explain, but basically you are duplicating what the original spring mount looks like, but bolting it to the top of the spring mount. This is enough to get by with kids in the rear seat, but still not enough for adults.
Next fix is simply going to air bags in the rear coil springs. Very little pressure is needed. No more than about 20 pounds will raise and stiffen the rear up enough for 2 adults in the rear seat. I like the air bags better than air shocks because you can buy high performance shocks and have good handling and normal ride when the air bags are lowered to a very low pressure when they aren't needed. You can also adjust the air bags separately to handle traction problems if you drag race.