In real rustic pieces like what youre describing putting hemp rope between planks will fill the gaps. This Old House did it in an episode a ways back. Plunge the rope in and stain to match. They did it in a not so rustic house and it looked ok but i think a cabin setting would look better. Also since sanding the floor after the rope is installed probably wouldnt work to well so if you do plan to sand id do it before installing the rope. Otherwise the conventional filler will crack and break out with the seasonal changes.

Keep at it! I cant wait to see how this turns out. We have a 1897 farm house here in TX that has floors similar to you. We are not sure the wood, as it is painted, and has been since my folks bought it back in the 1980's. I have not yet had the time to start the stripping process but I would love to one day. This house has a lot of history, as 11 children were born and reared here. I am afraid of all the sanding, to get some boards even but I want to leave some of the wear, as it has character. One room at a time may be the way to go. The bead-board was once painted grey (by the previous owner) like the staircase the original was stained (one room upstairs still is)and we painted it white. The banister is original. The treads are all hand cut by the builders. I want to restore them first. Here is the house itself with new Hardie-board siding

As someone who used to have an old house about that age with pine plank flooring and now has carpet over plywood subfloor it makes me cringe to think of painting it. Is the floor unfinished? Can't you just finish it or get it finished? I have seen lots of pictures of painted floors and some look very nice but think how much other people are spending for vintage pine floors like you already have. Barbara

All of our "change orders" were via email "credit" for work not to be done, while I (as an attorney no less) believe in documenting as much as possible, my takeaway from this fiasco is that in the end the more important thing is to get the most competent contractor who is also very honest and a good supervisor and responsive and trustworthy and a good partner and then document as well as possible. On the documentation scale my contractor was a 6 or so- not seat of the pants, not all buttoned up. So I have paperwork catching him in what I consider to be semi-fraud (taking a deposit for one thing and 2 weeks later trying to turn it into something else) which was the real reason I had to let him go (the floor stain problem was one of the problems but the bigger one was poor supervision, poor communication, poor work quality by the workers not caught by the owner etc.). Enough was enough. I've since fixed the floor stain via floor specialist, gotten my own electrician to get power to outlets that didn't have it (kind of important for the dishwasher outlet to, uh, have power before dishwasher is installed, etc. etc.), gotten a plumber to move the sink pipe 3" to the left and to move the range pipe up or down to the right place and put the shutoff valve near the wall not near the range (it was reversed... reversed!), etc. So many examples of this. My new kitchen contractor is a trusted time/materials guy who's a carpenter who does all but plumbing/electric so I'm basically the GC now. I'm finishing the job (kitchen should be done in a half week, countertops and all) and will fight with the guy I left behind when I have more time after we're all moved in. I ran into a neighbor - turns out the contractor's partner destroyed a grout job in her bathroom so she has to re-do the whole thing 3 years later, he scratched up her tiles. She is the only person I met who even used these guys, so that was further confirmation that I'm not crazy and these guys either can be hacks or can hire inadequate workers and not supervise them properly which is at least PARTLY what I think happened with me. No matter how careful you are a lot of it comes down to hiring properly. I usually hire well, this was a HUGE exception.