Your first complaint is common....because it is normal for these tractors. You can somewhat solve the problem with two short 3/8" bolts, 4 flat washers and two 3/8" nylock nuts. Install a bolt with a flat washer through the long slot. Put another flat washer on the other side and add the nylock nut.
This shortens the length of the slot, causing the lift to pick up the deck sooner and thus raise it off the ground more. Keep in mind that when you put the deck down on the ground, you need to move the lift lever so that the pin that lifts the deck is sitting in the middle of the slot. This allows the deck to float up and down during mowing.
Send me an e-mail and I will send you the Parts Manual for your tractor and the clutch manual. The parts manual should help you figure out if the clutch linkage is assembled incorrectly or not. The clutch manual will help you determine what might be wrong with it.
I will also send you an Op manual for your mower deck that will explain how to set it up for the optimum cut.