Don't make decisions on that motor based on my input ...I'm asking questions, not answering them! I would just look into it a bit and find out for sure what the whole story is before committing.
Diesel is compatible with epoxy, so you should be able to build your tanks. Tanks outboard or inboard of the outer bearers (web stringers) should be fine. Outboard will slow roll a tad but "in the noise" if you know what I mean. How much fuel are you thinking of? Keep it amidships or slightly aft, e.g. don't put it forward nor all the way in the stern. Also ...check with your insurance company. Sometimes homemade built-in tanks increases insurance costs, e.g. a repeating year after year payment, while commercially built tanks don't ...the long run savings may more than pay for the commercially built tanks. That's IF the insurance rates are higher for built-ins. Check and see... Most insurance companies are not keen with 'I built it myself'...
Brian