I suppose there are a lot of ways to do this. I will share my thoughts. Of course I expect people to do what best suits them.
For starters I would use a 3" high speed pneumatic cut-off wheel to cut the welds and remove the pipe. Almost an instant fix. Cut-off those eye bolts sticking up too
Next (as time passes) remove one of the plates and fill the holes with as large of a stainless steel hex head bolt that will fit. Use stainless steel washers and hex nuts (of course). Between the washers and the hull, use the type of thru-hull-sealant you see in the inside-rear of the hull
Your ski looks exactly like mine. Not surprising since Yamaha has produced and sold over 1 million Waverunners. That equates to a 10 billion dollar revenue. I like math
My FX140 is one of my hobbies.
My postings are personal opinion.
My opinion's are not professional advice.
Jet ski owner - rider - maintenance - 17yrs.
2002 Yamaha Cruiser FX140. 1000cc.
2017 Lowes Stryker 16. Mercury 50hp
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