I have fitted a 41 tooth rear, but kept the standard chain. Wheelbase is shortened by about 7-8mm max. It's made no noticeable difference to the handling or stability, but it definitely makes the engine livelier & more fun.
If I was to change it again though, I'd go for the 42 tooth (with std chain) to make a bigger difference.
I don't understand the stability argument - is stability (or lack of) actually a problem on 749/999 range

As for JHP's recommendation of 500mm from swing-arm pivot to centre of wheel, I'm sure it's very good advice for the JT's/ RL's/ NH's of this world, but I sure as hell ain't gonna notice the difference
Gimpboy....welcome to the message board & congratulations on your excellent choice of bike.
I'm puzzled though, why would you want to revert back to std gearing

If there's one thing people on here agree about it's that it is over-geared as std.
As for the alarm, I agree with KeefyB. Bite the bullet & buy a new one. Most of the cost when buying/ fitting an alarm is for labour. The actual alarm costs approx £85 +vat. So say the alarm costs £250 fitted - £150 of that is labour for fitting which you'll still have to pay for (+ cost to remove from the CBR6).