Some good news.
I tried DVLA again yesterday and they confirmed a case had been opened for my reg application (so not lost in the post). I also was contacted by someone from the kit & rebuilt dept later to say that everything in my application was fine apart from the kit receipts not showing the VIN number for the chassis or confirming that the chassis was part of the kit (it just says module 1, 2 etc).
I thought I'd have to give Marlin a call and ask Terry to send a letter out but I found the delivery note/part sign off sheet from when I picked the chassis up and that did have a full list plus the VIN. Emailed that to DVLA and they said they'll accept on this occasion though normally they want the certificate of newness from the manufacturer (thought that was just if you were after a current plate).
So, one to prepare for if anyone else is getting to this stage soon, better to get the info off the kit manufacturer up front. It doesn't actually say you need this type of evidence on the application guidance which doesn't help, just 'receipts for major parts'.
They've also confirmed I'll get an age related plate and won't need to tow it to get inspected again
, though I'll be suspicious about the latter until the V5 is in my hand.