IMHO a late 80's Mako 261 is quite possibly the best center console to do a restoration with customization. To this day, the 235 and 261 are reviled as one of the nicest riding hulls ever designed!
Break it down, replace/repair the transom (if needed), put a nice transom bracket from Stainless Marine, recess all the deck hardware with pop-ups and such.. I could go on and on, but you get the point.
There is a great website with TONS OF INFORMATION by people who did and are doing just what you are looking to do. Trust me, these guys that already done a Mako restoration have all the answers you could ever want..
http://classicmako.com
Sure Whalers are great boats too, but I wouldn't go with one for what you are looking to do. They older ones always seem to cost too much if you want to do a restoration and that means less money that could have gone towards a nicer GPS or a Radar. The whaler could also be a little tougher customize to your liking. If you decide to go with a Whaler, you can always go to the classic whaler website..
http://continuouswave.com/whaler/
Good luck and looking forward to seeing the documented progress on whichever you go with.
EDIT - One more thing, a Mako can handle a second station no problem, but will have some roll (as will any boat like that).. Just figure out what it is you want from the boat - a smooth ride at higher speed or a slower ride with smooth trolling and idle characteristics?
More deadrise = smoother ride, but more roll at rest/trolling.
Personally, I'd take the faster and smoother ride of a deeper vee over a slower and more pounding ride of a wider beamed and flatter keeled boat. When the WX gets nasty, people usually want to stay to the last minute, but often cannot and that is where the luxury of speed comes in.
As for motors, check out the Verado's.. For a second station, they are ideal since they are electronic shift and control with auto sync and the ability to integrate with GPS, autopilot and radar.
