If your engine installation will be much more than about 10% heavier than the original, you should certainly look at possible reinforcement of the pickup points in the fuselage and absolutely so if you intend to do aerobatics.
As a general point, it is probably not a good idea to install an engine package which is a lot heavier than the standard Lycoming, it just creates many more issues for you. You certainly need an accurate weight and C of G for the engine/ gearbox/ prop you intend to use plus dimensions and I'd say you should not start at all until you have everything in the flesh, rather than just drawings.
It does not hurt to use the longest available cowling in most cases unless your engine is a very different shape and you need to custom build that too.
Since the gear mounts are integrated into the engine mounts on RVs, it is often easier to use these portions of the stock mounts, cut off what you don't need and progress from there. If you go this route, try to ask for a non- powder coated one as this will save you many hours of stripping. The gear mount spigots are very precise and hard to duplicate without distortion during the welding process.
As far as getting all the angles right, this takes a lot of time to set up. For my RV10, I built a special stand to hold the entire engine and gearbox from the prop hub while measuring and mating to the fuselage, others have done it vertically on a firewall mockup. Neither is really easy or fast.
Here is a link from my old RV6A project page which shows some details of the process:
http://sdsefi.com/rv4.htm
You may find this page on isolators useful too:
http://www.barrycontrols.com/product...m?cid=1&fid=47
I'd be interested to know what engine you are contemplating?