I recently bought a used Ascend FS128T and I'm going to remove the stock rod holder and lower and lengthen the anchor trolley and want advice on the best hole filler to use?

For small holes I used Marine Goop. Anything larger I would seek advice from the manufacturer. In many cases they will send you filler material to match. I once owned a Cobra kayak and had a crack on the end. I contacted Cobra and they sent me the plastic welding rods and instructions on how to fill it properly.

Also, if I'm not mistaken, many of the local kayak dealers will help you make the repairs for a minimal fee.

I weld mine with a soldering iron and use the plastic wire ties for welding rods. Depot has different colors of wire ties.

If you ever use a hole saw to install flush mount rod holders you can save the plastic and use it for small repairs.