Engines are pricey - I have an 06 WaveRunner FX HO - I just put my 3rd engine in it, found a wrecked 05 FX HO and paid $2k for it at 200hours to harvest the engine. Which was a deal - these things don't let go nicely - they detonate and usually take the lower cases with it. Used engines are sky rocketing/remans are going up because the lack of cores are becoming common.
My 2nd engine was an SBT motor that let go (was in it when I bought the pwc in 2011, was told it was rolled over and the original engine was flooded/ruined) - so make sure it doesn't have remans in it and they are the originals. I keep telling myself the 2nd engine popped because it was a crap reman and that's believing the story the first engine was trashed after 60 hours because the original owner rolled it over the wrong way.
I've heard stories of these engines going 1000 hours in rental skis.
Issues you may run into - fuel injectors - they can become clogged and if you ignore them, you will lose an engine. They should be cleaned every few years.
Poor regulators / Stators - depending on the amount of hours - it's possibly you may need to invest in some charging system components in the not so distant future.
Also they're dry sump oil systems, oil level is either completely wrong or perfect. If you put oil in to the point of proper level when cold, you'll ruin your air filter. Do some studying if you get it.
Although pumps have the luxury of not hitting the prop when going shallow - the impeller and wear ring need very minimum clearance. Shallow water usage usually sucks sand/pebbles past the impeller which will degrade the performance of the pump. As far as maintenance goes - if you're not over zealous with the throttle in the shallows - they're pretty much maintenance free - there is a sand filter for the water inlet which can become clogged and need a cleaning.
Avoid usage where there is floating vegetation, otherwise you'll be swimming under the boat and clearing out your intake grate.
Honestly - if I was to do it again, i'd find myself an NA 1.8L Yamaha - the MR1s are decent but I don't think i'd buy another MR1 powered water craft. But I think that's my recent experiences souring me on them.