Very different carbs - the BN vs TM Mikuni. TM has a throttle slide with needle as well as a float in the carburetor, while BN have a butterfly with pop-off regulator without a bowl/float. TM run either gravity or pumped with a vented fuel tank for fuel feed, and BN run closed circuit (Ventless) pump feed only. BN pumps are right on the carbs, while all dirt carbs are either external pump or gravity feed. Most BN38 pairs only have a single pump feeding both carbs where-as larger BN and SBN (Super-BN) carbs will each have their own pump. Jetting specs between BN and TM will be completely different as well. The pilot and main jets are completely different series, and then of course you have your pop-off which is dissimilar to slide/needle on the dirt carbs but act similarly fueling wise. BN carbs can run up-side down (Which is why they are used in JetSkis), without leaking fuel out, but TM/VM need to run right-side up and have overflow-vents. The BN carbs also have a LOW and a HIGH FUEL screw, whereas the TM only have a LOW AIR screw. Very different. I don't see why they would not work except as noted - not the greatest protection from dirt.
Tuning BN/SBN carbs, you want to tune your pilot jet and pop-off with a TARGET of 1~1.25 turns out on the LOW FUEL screws else you're not at the right spot. High screw needs to end up at about 0.75 turns where at ~1.25 turns the
Engine 4-strokes from being too rich - so start at 1.25 turns and increase main jetting until it 4-strokes, then close high screw down 1/2 a turn to the 0.75 target.
Screws in more than .5~.75 turn means you need to DECREASE jetting, and screws more than 1.5 turns out means you need to INCREASE jetting.
If you are going to run a set of dual BN38+ carbs, and each carb has a fuel pump - I STONGLY suggest drilling out the restrictive returns within the pump side of the carbs with a 3/16" drill bit, and then run a single restrictor (Mikuni BN style size 60 Main jet) in the return-feed collector (1/4" Y fitting), else you could have an imbalance of pressure and trouble pinning the correct pop-off and ultimately carburetion between the pairs - (Meaning carbs will be 'off' sync fueling-wise from each other.)
Also a known fact in the twin jet-ski world is - a big ass single carb usually works out much better than dual smaller carbs on smaller displacement engines (<700cc) - that is if you can get the single carb manifold. Dual BN38s won't always perform better than a Single SBN46 or SBN48, and then a single carb is 5x easier to tune than duel carbs. Single eliminates throttle linkage issues, synchronization issues, 3x the fuel lines, twice the problems, space problems, intake hook-ups... single carb may make our swap more achievable given 'Frankenstein' installations. Single bigger carb usually hits harder torque-wise in the low to mid range making it ideal for trail and short-track. Maybe go DASA/Full-Spec SBN48, or Full-Spec SBN49/50, or duals for a desert runner I guess.
I suggest running a single SBN46 or larger actually; and I can help with tuning if you need. Given the goal is about a 600cc Engine, there should be no need to run bigger than a single SBN46. You can get a single SBN46mm carb brand new for about $300 from
http://www.blowsion.com or if you can find a used mid-90s Mastercraft WetJet Kraze jetski - the whole skis can be found on a trailer for about $500. Always use Genuine Mikuni rebuild kits for BN and SBN carbs.