Hi guys,
Many thanks for the replies
Seems to have been a combination of several factors, the first being the dowels holes/ threads were still full of crap from the vaqua blasting I had done on the cases.

Fortunately for me there is a good sized ultra-sonic tank where I work, was able to drop them in and let them fizz for a while. The down side to the dip in the tank is that the fluid used stained the cases a blotchy gun metal color. :roll: So then had to spend the next few hours trying to get them back to some sort of uniform color. It was weird, as I've used this tank to clean up other parts and they've come bright and shiny..Dunno.
I think the other factor was until I'd screwed in the long studs, got them seated in straight, they were pulling the cases very slightly. The upshot is they now seem to fit together nicely. I did a trial fit of all the case screws and bolts (including the front and rear isolastic bolts), there are no gaps at all. Whew!
I managed to get the cases heated up and put the mains in. Next job is to assemble the crank. I thought it prudent to unpack and check the barrels, only to find that post honing no-one had thought to drop a bit of oil down the bores to protect them, they've freakin rusted! It's not as if they'd been left in a damp place, like the garage. I'd kept them in the house, carefully packed away. So they've got to go back for another hone.
Oh...And while I'm having a moan...I bought a brand new front isolastic case....It doesn't fit. It properly doesn't fit (not just excessive powder coating), so that has to go back and get exchanged. I'll take a pic and post it.
Sheesh talk about some hard lessons to learn. :evil: