the problem you may have with putting weight on the mould, or that I've had using clamps is that you only have several seconds before the kydex cools to the point which it will not form well. Its possible the reason your moulds were not coming out well is that you waited a little too long and it wasn't flexible enough.
What I do for my moulds is I take some pink insulation board (the solid panels you can get at home depot for $7 a piece), and cut a mold fit for the knife out of 2 pieces, so they close tightly. This allows you to make different parts of the mold tighter or looser, and it also gives a very tight form. If they are coming out a little too thick, wrap a piece of thin cloth around the knife, but don't loosen the mould. I heat my kydex in my oven, so i wait for it to get soft and then put the mould together in the oven so it stays soft, then pull it out and apply pressure between the floor and my foot. With bigger knives, I use just a piece of wood in between the foam and my foot.
The only problem with this technique is you only have one good shot because the heat from the kydex makes the foam expand, which ruins the mold if the knife isn't in place well, but helps when it is. They do make heat resistant foam in a few places but its expensive and I can do like 10 moulds for $7