Solved. I'm going to write a detailed solution here for anybody googling years into the future. I will use photos but also text for longevity.
To remove the water pump on the honda nc700, you need to do more than what the service manual specifies. Class, turn your books to page 8-12:
https://www.manualslib.com/manual/1106110/Honda-Nc700xa.html?page=291#manual
- Do all the steps the manual mentions on this page, so drain coolant, remove radiator and cooling hoses. Now is a good time to replace your hoses, my 2012 coolant bypass hose [19322-MGS-D30] was especially crusty. You don't need to remove the frunk on the nc700s to remove the coolant bypass hose; instead I unclipped the evap hose from the clutch cable bracket and dug the hose out with trim picks and a screwdriver.
- Unclip #1 spark plug wire and drain hose from the front lower frame rail
- Remove all the water pump cover bolts. Three will come out easily (90006-GHB-730 and 2x 90006-GHB-690), two will hit the frame as you loosen them (90006-GHB-700). It might be an idea to order two of these in advance in case you want to cut/file the heads off to ease disassembly, but then you will be back to square one come reassembly time). I used pliers to continue turning the bolts maybe 1.5 more rotations after they touch the frame, so they are digging into the frame, but they will come out. You can wiggle the water pump assembly out of the head while you do this, to help get some angle on the bolts as they squeeze out of the head.
- Once the bolts are out, reinsert the water pump assembly into the head.
- Now remove the outer painted housing 19221-MGS-D10 partially, still holding it within the frame and remove dowel pin 90704-MGS-D30
- Separate and remove center plate 19231-MGS-D30 from the outer painted housing
- Now you can remove the outer housing by rotating it down and forwards out of the frame
- Now remove the inner water pump assembly from the head and remove it from the engine.
I found an oil leak I didn't even detect was there. There was a fair amount of corrosion as you can see in the attached pictures, however I can't tell whether that is due to wrong coolant type (bought this bike with green silicated coolant in it, hence why I am doing this job, and replacing it with genuine honda coolant) or just due to age. I am replacing all three cooling hoses, flushing the radiator, and replacing all the water pump O rings, copper washers, and gaskets.
List of part numbers:
Water pump:
TWO - GASKET, WP BODY 19226-MGS-D30 - $7.75EA - EX JAPAN
O-RING, 22X2(ARAI) 91301-GK1-003 - $4.35
O-RING, 48X2.6 91301-MGS-D30 - $4.45 - EX JAPAN
TWO - WASHER, 6.5MM 90463-ML7-000 - $4.00
Thermostat:
RUBBER, THERMOSTAT 19305-KV3-010 - $8.30
O-RING, 30MM 91356-425-003 - $7.75
HOSE, WATER BYPASS 19322-MGS-D30 - $14.95 - EX JAPAN
Radiator:
HOSE, RADIATOR UPPER 19505-MGS-D30 - $14.40 - EX JAPAN
HOSE, RADIATOR LOWER 19506-MGS-D30 - $21.35 - EX JAPAN
TUBE, 5.3X580 95005-55001-20M - $28.45
TUBE, 5.3X250 95005-55001-20M - $28.45
THREE - CLIP, TUBE(B10) 95002-02100 - $2.50EA
PACKING, RESERVE TANK 19107-GET-000 - $5.95 - EX JAPAN