You have the opportunity to completely renovate the pond if funds allow. I would certainly consider scraping all the plant life and the soils that they are currently growing in out of the bottoms. This soil is likely all the sediments that washed into the pond over the years of it's full life and these sediments will have a lot of nutrients in them that could cause problems once it's filled again. Excess nutrients tend to aid in the production of nuisance algae. Do a little reading on FA (filamentous algae) and you will understand very quickly how important it is to avoid making conditions favorable for it's growth. If you choose to de-muck the pond, make sure you do not dig into the original clay bottom very much as you could compromise the seal and create a leak.

It looks like you may have some water left standing in the pond in places and I would try to get that to drain out first so that your excavator will not have trouble dealing with the soup. That pond muck is some slippery stuff. Make sure that the water does not have fish in it now or they will be there once you fill it back up and that can be troublesome if they might be GSF (green sun fish)or BHC (bullhead Cats).

Like RAH says, do the drain system right the first time so that it does not cause problems and expense down the road. It's much harder and costly to correct a failed drain when the pond is full of water.

Welcome to the club, you have come to the right place!

Fish on!,
Noel