if wanted to improve (ie, change a window to French doors) can we do this out of SMSF cashflow?
My understanding is no, you couldn't. That would be considered an improvement. My understanding of repairs is that you upgrade/replace items to something akin to the original. You can repaint the walls and whatnot, for instance.
Note that this is only when an LRBA is in place. Once the loan is repaid, you can do whatever you want. I would recommend you read the link I posted from DBA Lawyers. I would also recommend you forget the ATO site and read Super Guide instead. SG and DBA are my go-to for super related stuff, although DBA may be a bit too technical (I work in the industry).
You are also correct, re: CGT. SMSF's (all super funds actually) have a concessional tax rate of 15% and a CGT of 10% for assets held longer than 12 months. Assuming they are compliant of course.
Also, I hope you have absolute confidence in your SMSF advisers (whoever they are). Especially going into something like you have proposed here. You need to be aware that as trustees, you are solely responsible for ensuring the fund remains compliant at all times. Pleading ignorance or saying 'But our adviser told us to do that' doesn't fly with the ATO. So be really careful who you get advice from and make sure they absolutely know what they are doing.
If in doubt, get specialist legal advice. It might cost you a fair bit up front, but could potentially save you significantly more in the long run.