If it does rain the key thing to worry about is chafing? So lots of Vaseline around seams and hems and under arms - and St johns ambulance always hand it out on course.
In 2009 I wore a vest and my arms were raw at the end -but I don't think long sleeves would have made much difference? Some people did have jackets around their waists which they put on when it rained - but personally I find that too much faff on the day? Definitely an old sweatshirt and a bin liner for the start.
They do have marquees and free tea at the start - it is a scrum but you can take some shelter if it's truly awful.
If you have proof of recent form then apparently you can get the pen number changed at the expo?
Might be trickly to run 3.45 from any part of pen 9 to be honest?
I always get into the Pen early and get to the front - then when they drop the tapes (about 15 mins before the start?) you can walk forward with everyone and will likely end up mixed in with other pens. Some people definitely push forward at that stage - and if I were you I think I'd do that and aim to get up to Pen 5 or 6? The congestion in pen 9 would definitely stop you achieving your goal.
DLR - there was one year when it broke down spectacularly leaving some runners to run to the start
Rain - I did one VLM (2009?) when there were huge downpours at mile 9 and mile 15 and then hailstones at around mile 20.... have to say the team spirit was great - lots of oggy oggy oggy and cheering ourselves on. If it does rain remember Vaseline is key..... You can't really plan apart from that - you just get wet and will need some nice dry clothes in your bag for the end - and maybe a small towel?