To fully repair Shelter you need to apply 97 upgrades.
Aim for the upgrades that take the least amount of time to complete like 10 sec, 1 min, 5 min, 10 min, 20 min and 1 hour.
For example there are 4 Box of Herbs, 4 Rat Traps and 4 Box of Plants upgrades - upgrading each of those 4 to 5th or 6th level each should put you on around 60-72 upgrades meaning you can split remaining 25-35 upgrades into first 2-4 levels of 9 other improvements without wasting too much time.
Personally I'd say avoid grinding resources for Electric Generator when going for this achievement as it's first upgrade takes 6 hours and requires and whole bunch of resources that you could easily spend on other improvements that require less time and resources to complete. Yes I'm aware it would let you do 2 improvements at once but honestly it's just much easier to manage 1 improvement at a time but again this comes down to personal preference and how are you with managing your time when waiting for those upgrades to finish.
Below I've added 2 pictures of fully repaired Shelter which looks super nice
compared to a broken down Shack you were given at the start of the game