I have a 1946 45" flathead that I am restoring. The frame and everything is new. I am not sure how to route the wiring harness. I would like to keep to the original routing as much as I can. I assume it didn't run through the frame as I don't see any holes through it.

 

I would think the main would be on the frame as on HD late models. You don't have your state you live in your profile and have some contacts which may help with your question and any future ones. One is "The Antique Motorcycle Club of America, POC: Ed Higgins, National Technical Consultant, 37 Riverside E., Sidney, NY, 13838", or, "HD 45" Restoration Company, PO BOX 12843, Albany, NY, 12212 @ (518) 459-5012". A good book (don't get thrown by the simplistic title) is “HOW TO RESTORE YOUR H-D” BY BRUCE PALMER III @ $39.95 It doesn't tell you "how to" so much as "what to" and has a lot of really great info about all the HD early models plus POC for parts if you're going for "original" restore! Another source is the V-Twin Catalogue for AM parts. Just FYI, I put some "hard-to-find" PN's for the 45 below:

6V BATTERY 66006-29F (still available from HD)
CONDENSER 1629-30 4303-29A
"RUNNABLE" S/P ND M17 CHAMPION D14,16 18MM 37-09B-E=RACING (not the originals: these can be pricey if you even can find)
COIL 1722-30A
S/P CABLES 1596-30 LONG, 1597-30 SHORT
CB TO COIL WIRE 1613-30B
GENERATOR LESS DRIVE GEAR 1501-30 OVERHAUL KT 1503-40
CUT-OUT RELAY 4786-38
3 TO 2 GEN BRUSH CONVERSION BULLETIN #418

 

Get the book by Bruce Palmer " How to Restore Your Harley Davidson" It has several good pictures and descriptions of the wiring routing and where all the proper clips go to hold the wiring to the frame. I used this to install the new harness on my 42 flathead when I restored it. I converted to 12V so had to modify a few things on the harness.