Are the comps for homes in good condition or those that need new roofs? If the former, I'd definitely factor in the cost of the roof. Think about what total cost you are willing to pay here... Are you willing to pay, say $130k (or whatever it is) for this house with a new roof and new windows?
Agreed. It's hard to value those things (quickly) if you haven't had the opportunity get quotes for roofing, HVAC replacement, tree removal, window replacement. I'd get free estimates on as many of those items as you can. And ballpark the rest. As dragoncar said, you can add those to your potential price and that's your price for that home with new roof, new windows, new HVAC, tree gone. If that price doesn't scare you, for the home in that updated condition, keep pursuing. Keep in mind, that price probably won't look as good, but it will be for a completely different house... all updated.
To me, and this is based on what I'm picking up from the info you've provided, the BIG things that this house has going for it are the location and the two full living spaces, allowing subletting with no work. I don't know the RE market where you are looking, but it sounds like both of those things, in conjunction, may be nearly impossible to find again. If we are talking about a location so good that you can walk to most destinations.... not just bike or have a short commute, is potentially HUGE if you plan to take full advantage..... maybe you don't. That requirement should really narrow down the options. Even if you expand your geographic area to include places that allow a short bike instead of a walk, surely there aren't many places for sale that offer 2 living spaces for a single family price, are there? Again, your local RE market may tell a different story. Maybe those things aren't nearly as rare as I'm imagining them to be.... or maybe you aren't even dead set on your house meeting those criteria.
Are the "comps" you are using to determine price also in that limited geographic area (allow walking)? And do they have 2 living spaces, ready to go? If not, then I'd be careful to hold your house to rigidly to those comp prices. I'll admit, it sounds like this place may take some money to get where you want it. But the ability to rent the place without having to drop any money right away, is huge in my opinion.