I followed the manual with regard to the engine bolts - that is I mounted some metal blind nuts (that came with the kit) at the back of the firewall on doubler strips and epoxied them in place and the mounts screw into the blind nuts. Is this ok, or should i try to remove the blind nuts and use bolts and nylocks instead?
The blind nuts are perfect for that application. They hold bolts that are tightened securely but you can also use lockwashers for extra peace of mind or you can use thread locker for even more security. What do you ment "...on doubler strips"???? If you added wood strips, they need to be fuelproofed or they may compress easily when fuel/oil hits them.
Also, the manual suggest to punch and drill holes in the mounts now (before the firewall is mounted onto the fuse) - is it better to wait as you have suggested? I can always (assuming I can get to the back of the firewall) remove the mounts and punch and drill the mounts later, although this would be a little harder than doing them now.
It's perfectly ok to wait to position the engine on the motor mounts until you absolutely must. It is much more accurate to drill the holes in the mounts with them off the airplane. Use a drill press and it's lots easier to get very accurate placement. Experienced modelers often wait until the very last to drill the mounts for the engine. It's a smart thing to do, especially if your model is not a scale model and you're wanting every scale measurement to be exactly like the original. Slight changes of prop location won't result in any real difference in flight characteristics. If you use blind nuts, it's easy to remove the mounts so it matters little if you do it now or later.
Is it easier to just move the engine an arbritary 1cm forward and hope that no dead weight in the tail is required? As i understand, the kadet senior is generally tail heavy anyway - and I am adding a tailwheel back there too.
It's actually not easier to do it either way. It's the same effort now or later. As for adding a tailwheel being a consideration, removing the nose wheel is actually more of a change. Both together will change the expected design distribution of weight. But you won't know if that matters with the parts and stuff of your particular airplane until it's almost done. And then if you've not drilled the motor hold down holes, you'll be better able to deal with what worked out with your part weights.