Welcome, Eric! Glad to hear that you’ve been bitten by the aviation bug.
I can’t speak to the specifics of the Comanche (maybe Steve Ells will chime in), but I do have a few general thoughts on your list.
1. Make sure you buy an aircraft that’s equipped with what you want already installed. It’s MUCH cheaper to buy an aircraft equipped nice GPS, autopilot, engine monitor, ADS-B, etc. than it is to buy a simple VFR airplane and install each of them yourself.
2. For your mission (XC cruiser, 2 people, good instrument platform), you’ve identified a couple of good options. Any of the Piper aircraft you mentioned will do a nice job. A PA-28-180 Cherokee or -181 Archer would also probably fit the bill; as would early Arrows.
3. Lots of opinions on auto fuel usage but I will say this – in the big picture of aircraft ownership, fuel costs are but a small portion of the total outlay. I wouldn’t consider this as a deciding factor.
4. The more you can fly, especially when you’re training, the better. From my perspective as an instructor, plan on lessons two times a week at a minimum (even if you don’t fly because of weather/maintenance/etc., you can do ground work). Sounds like you’re planning to do this. Great. Frequent flights will save you a huge amount of time.
5. A $60k budget seems reasonable. You may have to make some tradeoffs to get the avionics you want (less horsepower, older airframe, higher-time engine, etc.). Do remember that the first couple years of ownership tend to be expensive as you work out the kinks with a new bird. Set aside 20-25% of the purchase price. There’s nothing sadder than watching a newly-purchased aircraft sit because the owner blew his/her wad and doesn’t have money to fix some relatively small maintenance issue that crops up a few months after purchase.
Another thing that you will want to work into your equation is insurance, especially for your first year or two.
For a zero (or low-time) private pilot, your insurance on a PA-24-180 Comanche, or really any retractable, is going to be pretty steep. That’s even true if it’s a high-performance complex (PA-24-250). Consult a broker for up-to-date costs but my guess would be in the $2,500-3,000 per year range for full coverage. As you gain time and certificates, that will decrease somewhat, but a retract is nearly always going to be more expensive to insure than a comparable fixed-gear aircraft.
Though you will also pay more for a PA-28-235 / 236 versus, say, a Cessna 172 or Cherokee 140, the difference won’t be as huge. A PA-28-235 is still a lot of aircraft for a low-time pilot, so expect premiums to be $1,500-2,000. Drop below 200hp with fixed gear and that number is likely to be $1,000-ish.
And now, a question for you which might help guide your decision – where will you be flying?
If you’re in the Mountain West where you’ll consistently be operating out of high-altitude airports (>5,000’ or so), the horsepower is a real benefit – some might even say necessity. There’s a reason the Cherokee 235/236 and Cessna 182s are so popular in the Rockies.
On the other hand, if the majority of your flying is in the flatlands, a 180hp or 200hp bird will do just fine and will still give 120-knot-ish performance at cruise. Four-cylinder engines are going to be cheaper to operate and maintain. The 180hp Lycoming is a great engine (I’m biased as I fly behind one).
RE: damage history. You will want to order the FAA records CD for any aircraft you’re seriously considering (https://www.faa.gov/licenses_certificates/aircraft_certification/aircraft_registry/copies_aircraft_records/). Major repairs should be documented with a 337 form which details parts and methods used in the repair. If they’re not, that can open a big rabbit hole, into which you will pour a bunch of money.
One more item to note – the commercial requirements have recently changed and a complex is no longer required for either the practical test or commercial certificate training. You won’t need a complex for the CFI ride, either. You do still need 10 hours of training in either a complex, turbine, or technically-advanced aircraft (TAA) per 61.129(a)(3). It’s not difficult to rent an aircraft for those ten hours if you don’t have one already.
I have dealt with Skywagons a few times and my experience was positive. They didn’t seem pushy and were straightforward about what an aircraft was (and wasn’t).
Hope that helps!