If you take your time then there are no problems to be had by cutting the looms and resizing to what is needed.
My loom had to be heavily modded as the battery, ignitor, fuse box, regulator all had to be moved. Also i fitted the speedo from a zx10r and had to mod the loom to accept this.
when adding wire it is not important about the colour but the guage of the cable needs to be the same, more but never less.
Remember to leave enough slack for the steering to go lock to lock.
Solder and heat shrink all the connections and you will no problems later with water getting in.
It is best to have a wiring diagram handy for your bike and make sure you study the loom a little before you cut as there are often more of one colour thats the same( like lots of red wires that go into different circuits). If your loom has these then a bit of masking tape and a note put on it at the places where the joins are going to be will make life so much easier.
It is best NOT to make all the joins in one place in the loom as it tends to make that section too bulky (kind of like a snake swallowing a pig). Instead stagger the joins as it will help keep the loom even in thickness.
I put convoluted tube around my looms to make them look a good bit neater, espeacially where the loom is seen.
Most of all take your time, if you have to rush you will fuc it up

This loom took me 4-5 nights to do, about 12-15 hours for the entire rewire (whole loom was done)