It has been answered but I will throw in my response anyways. You will definitely need a new top end. It also wouldnt be a bad idea to have your cylinders sent off the be re-plated or sleeved. If someone else could answer that, please do. For example, the cylinder in my YZ 125 is plated and you have to send it off to a cylinder repair company to get re-plated after it has worn out enough. If it is sleeved, than they will press the old one out and install a new one.
Since you have such low compression, I would definitely imagine some sort of scarring or damage to the cylinder walls. Attach some photos if possible so we can see what they look like. It is also important you have a professional size your piston correctly to your cylinder. if it is sized to small you will get piston slap in a loose bore and eventually it will explode in your cylinder sending chunks of piston everywhere. If it is sized too big, it will expand too much when hot and seize in the cylinder. either way, make sure you have someone knowledgable do that. If you send them off to be repaired, they will take care of that for you.
As for your carburetors, the needles, seats and o-rings are essential to rebuilding the carb just like everyother piece. If you did not use genuine mikuni parts, they will fail the pop off and leak tests. I too have a 96 GTX meaning the components in your carburetor have the potential to be 24 years old at this point. The internal parts of a carburetor are considered a wear item and simply will not hold up for 2 decades. Unless the PO showed you paperwork or a receipt that showed he rebuilt the carbs, assume they have never been touched.
Just to sum it up, you will need new top end parts and most likely repair to your cylinders. Also make sure you replace every internal part of the carb with genuine mikuni parts and you should be good to go