Hi,
1. Regarding the quantity box, I think that some code like this will do the job :
.hikashop_product_stock td {
vertical-align: top !important;
}
2.
- For the payment line :
.hikashop_payment_methods_table td {
vertical-align: top !important;
}- For the shipping line :
#hikashop_shipping_methods td {
vertical-align: top !important;
}
3. And for your Edit button I think that the problem is coming from the code of your template 
bootstrap.css file :
.modal {
  position: fixed;
  top: 10%;
  left: 50%;
  z-index: 1050;
  width: 560px;
  margin-left: -280px;
  background-color: #fff;
  border: 1px solid #999;
  border: 1px solid rgba(0,0,0,0.3);
  *border: 1px solid #999;
  -webkit-border-radius: 6px;
  -moz-border-radius: 6px;
  border-radius: 6px;
  -webkit-box-shadow: 0 3px 7px rgba(0,0,0,0.3);
  -moz-box-shadow: 0 3px 7px rgba(0,0,0,0.3);
  box-shadow: 0 3px 7px rgba(0,0,0,0.3);
  -webkit-background-clip: padding-box;
  -moz-background-clip: padding-box;
  background-clip: padding-box;
  outline: none;
}