My longest transaction waiting is before the segwit , took me a 1 week of waiting, that time blockchain was so lag. After the segwit its only 1hr. Shapeshift took you a day to receive? I guess the problem is in their system not with the blockchain.
Whats the longest wait you've had for a transfer to go through. I used shapeshift late last night and it still hasn't come through. I just did another one and it went right through.
The blockchain never goes down unless and until the hard or soft fork is occurring because it's being deployed with new algorithm when that happens in first place. Then we can off course expect the transaction to be slowed down as miners won't be at work as the master is sleeping. ;-)
Anyway for the shapeshifter problem I believe it's just the fees or may be it could be just shapeshifter itself. That doesn't look big problems and that could happen once in while. You should create the support ticket if the problems not solved yet.