Your color scheme idea sounds bold and beautiful. Try it on for size at Sherwin Williams or Benjamin Moore website. You can upload your photo and try out visually. But, I'd probably play it safe and do a beige with white trim. There are a lot of board accents and I'd like to minimize the contrast. Something like this...

I like Darzy suggestions. A earthy tone to go with the landscape. I would want it to complement the surrounding instead of stick out like a sore thumb. Maybe a few window boxes to soften help blend nature with structure.

I would remove the angled brown boards. It looks like a poor attempt at a Tudor style. I agree, scour web sites like houzz for colour ideas. Also, all paint stores have done a great job of creating booklets with great colour combinations.
The rule of thumb is a subdued main colour for the largest areas, a secondary colour along the same tones for accent and a knock out third colour for smallest areas like shutters and main door.

Yes, ditch the boards. What a gorgeous building (polite envy)

Having just painted my very small home, I fear your budget might be a bit tight -- I was shocked at the cost. There is probably lead paint which can escalate the cost significantly since the contractor has to do extra work. And it's not worth it to skimp on prep or quality paint. You can keep the cost down by keeping the color scheme simple. It's a wonderful building and will look even better with fresh paint. Congratulations!

I would look at craftsman paint schemes. Is that stucco on the half timbered wslls? If you don't like the half timbered look, paint the same as field. Or just a small percentage darker.

Save the color contrast for doors and windows trim. Look through Sherwin Williams historic craftsman exterior colors, ad well as others. Some craftsman homes used stucco and half timber, though perhaps not quite in the same way as this home.

What a beautiful reuse of an existing structure

Congrats.

You have a challenge and your budget is not sufficient. So, what to do? I would go to local historical society and find pictures of the original structure. Try to stay true to original look. Don't attempt to remove the angled boards. That will lead to domino affects that will cause more work potentially. Has the inside been restored? Electricals? Plumbing? Roof looks in pretty good shape? Not sure what is causing paint to peel? Could be water intrusion, or just lack of good maintenance. Is this going to be your principle residence? Get a good feel for everything before you jump into painting. Might be some hidden issues that take priority over painting. Research colors from early 1900's. I think you will find more simple colors and trims. Only Victorian's used many different colors. Also Arts and Crafts movement was a bit later as well. Since I "restored" a Victorian home built in 1900, I have been there and done this. Rewarding but took us 10 years! Do your homework, and you will save a lot of money, make fewer mistakes, and have better outcomes. Good luck!

Get rid of the Tudor wannebe boards I love your color scheme . I am so jealous i always wanted to convert a church. Make sure the garage doors are also painted to match no white there.Pratt and Lambert have a really nice exterior color combo you might want to check it is a little more on the taupy side but I have used the combo a few times and it is really lovelythey are in order bayberry, silver blond, pagoda red.

I like both of the schemes shown above, though with so much field area you might want to look at a green like sherwin williams light sage green, with roycroft vellum trim. A little more subdued, a little less yellow. I think Patricia's scheme has the right earthy tones...substance without flash, and the arch widows would become the stars.

Though I suspect the craftsman touches to your home were added (like the trim around the dormer windows), they're true to the time period of the structure, and the paint scheme you suggested you liked fits the earthy, often subdued colors of Craftsman homes. By 1915, Greene and Greene had designed some of the iconic Craftsman residences in the US, and one could order a precut Craftsman from the Sears and Roebuck modern homes catalog. I'm fairly certain your church was painted white in 1915, and I doubt that's what you're interested in.

You've certainly found a unique and beautiful home. Hopefully, the peeling paint is just bad primer, but you'll of course investigate the cause before repainting.

If you keep the craftsman details, I would choose similar colors for the siding and trim.

...and because you mentioned these colors...

I prefer the first pic.