John
Good question!
I removed the end part of the ovolo on the stiles, except where the ovolo on the rails would meet (see later) and then jointed the flush end of the rail (with tenon) into/onto the flush face of the stile (with mortice). Besides not having a scribe router to match the ovolo, I figured the additional strength of a fully scribed joint was minimal (gluing end grain of rail) and any twist could be resisted by a good length tenon and haunch. Where the ovolos met I considered just using a mitre joint but ended up scribing (using a narrow chisel for the curve, as I didn't then have gouges) - that is cut-away - the ovolo on the stiles, so that the ovolo on the rails went over/underneath. This gave a neat joint that was less likely to open up as a mitre joint might.
Now that I have a Router table, I purchased a matched ovolo/sash scribe set from Wealden's. This worked well, until I got cocky and just hand-held (to the sliding mitre gauge) the rail I was scribing. Of course, it slipped a few mm's and I removed more than intended - but that's why I have a good supply of filler :shock: (windows were to be painted). I reverted to using a clamp and all was well again.
As regards making stock all the same thickness, I found the 50mm nominal wood (from Champions) to come out at 43-44mm, so ran it all through the thicknesser, ending up at a smidgin under 43mm. I see you need 40mm. Doable by hand plane I suppose (just one window?) but let me know if you want to use my PT (or I'll do it). BTW I have some second-hand redwood (44mm thick, good stuff but painted) from the old window and french doors that might suit your needs - again, PM if you think it might be of use (cut/thicknessed to size of course), otherwise it's heading for the dump.
Your order of steps remark made me smile. I had/have the same problem. Keen to try out my Router table I cut the rebates and ovolo in the stiles and then struggled to cut the mortices (by hand) as one edge was only circa 10mm wide due to the moulding. This time I intend to cut the mortices then mould.
Good luck.
Mike