Hi Michael,
No problems cutting the spokes in situ, as everyone has said. I make all my own spokes and, particularly when calculating spoke lengths, always make them a little longer (better to look at them than for them
). You can use an angle grinder but I usually use a ball cutter in the die grinder, which works good for me.
With regards to your flat spot in the rear rim, if it's only on the outer lip, try a piece of timber on its side, giving it a good wack with a sledge hammer on the cross. The longer the piece of timber the better.
I've straightened many rims this way. You will need an inflated tyre on the rim and all the spokes tight before you start.
Good luck with it and I'm glad the front rim worked out for you,
Pete.