I have a 2002 23se. Nothing in particular to the boat itself i'd be especially concerned with - just the usual "tells" pre formal survey. I like to eyeball the bilge and any thru hull fittings, the fuel system (excessive rust, corrosion), and the electrical panel. I open the access port over the gas tank and take a good whiff - should smell like plastic/foam etc - not gas at all. Any additions or removals to the hull/cockpit, anything mounted on the transom, any additional rod holders, cooler mounts, etc. I like to eyeball and tap with a quarter etc to see if it seems solid etc. On a parker, I look UNDER the gunwale - you can clearly see the underside of anything thru/mounted and get a good sense of the general conditions the boat has been exposed to over the years. if it looks original and solid under there, my guess is you are off to a good start.
Having purchased and passed on several used boats over the years, IMHO, nothing can replace the small investment in a good, objective, professional surveyor's services.
Engine wise - I'm a fisherman, not a mechanic - but I have heard there were dry exhaust issues specific to pre 2006 Yamaha F225s and - although more or less "rare" / not widespread, were very material issues. There are specific inspection methods to evaluate if the motor you are looking at has these issues. I have an yamaha hpdi 200 on mine and its a great match. F225 i'd expect would be good too. I will also "defer" to an objective professional on engine inspections before closing a deal.
As a sense of perspective, my end goal with any used boat purchase may be different than yours. I want to get in, turn the key and go fishing and have a very basic, functional, solid, safe, reliable platform underneath me. Superficial wear and tear I am not so concerned with. I want to know the boat still has good "bones". You may have far more skills and tools than I do with respect to projects and related.