Hey John, I'll do my best to help however, there are many individuals here that I hope chime in with better ideas.
Seating - since we can't really see what you have (other than a bench in the house), what are you looking for that you don't have now? If you are refering to inside the house, I actually built my owned seating structure (it' on classic parker) and purchased Springfield seats. These were for the helm and I added a bench.
Rod Holders - if you are looking for gunnel mounted rod holders I would either get Gemlux or Mate Series (you can search for either on Google). Both are of good quality if you get their stainless holders. Both will be bale to handle heavy fishing too, if you get the stainless ones. I recommend only adding rod/cup holders (you always need a place to put your drink when the bite is on). (By the way, I have never heard of 90 degree rod holders. 0, 15, & 30 is what I am familiar with, unless you're talking clamp on)
https://gemlux.com/collections/fishing-rod-cup-holdershttps://mateseries.com/product-category/stainless/
Electronics are a preference and there are better individuals on here to point you in the right direction. I am pretty certain I know which ones you have now (the raymarine) because I had those older ones on a previous boat. They are good but not the most user friendly. I have had Garmin (not the new nicer ones) and Lowrance. I really like the Lowrance if I compare them to my older Garmin and ray-marine but my Lowrance was newer. I hear that the new Garmin are very user friendly as are the newer SIMRAD. Ray-marine doesn't get as much love nowadays and you tend to pay a premium for them. Somebody will chime in on this I believe.
As for the rest of your "wants", I didn't have any of them because I never felt a need where I fished (inshore Chesapeake Bay & Potomac River).
Best of luck dressing it out and I recommend sharing more information of what you are trying to do (seat wise), where you plan on fishing (Ocean, inshore ...), and target fish (Rockfish (striped bass), Tuna ..........)
Also, I would ensure that you have that motor scoped to ensure the mid section corrosion issue common with 2002-2006, 200-250 Yamaha's has either been addressed or isn't present. Your previous owner of the boat may have already addressed it (hopefully) but if your not aware of this issue do some research on it and check it out.
Enjoy