Multi fuel stove problems
As far as the smell your installer is correct, the paints and cleaners on the stove need to out gas. This can take a few hours to a few days depending on how hot you get the stove. When we used to install stoves we use to warn folks not to get the stacks above 500 deg and would leave a magnetic temp gauge on the stack. For inserts we recommended a bulb type gauge that could be placed on the stack and the gauge could be routed to the front.  Getting a rip roaring fire can cause damage to the stack, a standard fire running for several hours can and will make most brick work warm to the touch and depending on the fans or just plain heat coming from the stove the mantle will heat up. Since you now have cracks the system should be inspected. I hope they added a liner (required in my area) if a metal liner was added and you did not melt it down it should be safe to use. I would get a mechanical bulb type temp gauge that has a range at least to 500f. And install that so you don't overheat the stack again. As for other cracks and issues we would need photos to be of any help there.