1) I'm currently doing Stronglifts split into 3 parts each day, my work is such that it is easier to take three 30-40min sessions than one 60-90min session (I work from home and have my own rack/weights). I do Squats in the morning, Bench or OHP around lunch and Barbell Row or Deadlifts in the afternoon followed by some bodyweight stuff. Is this okay or should I be doing them all at once?
Erm... my personal take would be to get it all over and done with in one go to get your metabolism cranked up as best it will go, and burn all those calories. The theory being you will burn off the glycogen and readily available sugars in your system and let your body get to work on the 'harder to process' energy source: fat. Gaps in training are a good idea to come to each exercises better rested and replenished (from a food perspective) and so better in principle for strength. 
There are different schools of thought on this, and as long as the level of work done consistently increases, you will achieve broadly the same results.
2) For the last 6 months I've been following an 16/8 intermittent fasting plan, mostly because I find it helps me eat decent food in the 8 hour window rather than grazing and eating rubbish. Is this a good system to follow?
It's one approach of many used for calorie/intake control. If it works, stick to it, but be open to change if it stops working.
3) Should I add in another cardio session of 15-20 minutes after my last Stronglift workout? (I have a rower and road bike that I can use).
You could, and I'd always advice (hypocritically) doing some cardio to keep your ticker ticking over nicely. However, if this is a hardcore session, you obviously haven't worked hard enough during your resistance training.
4) Is there a better program than Stronglifts given that I want to keep running?
Why do you want to keep running? It's bad for your knees, bad for your mobility (tight muscles) and puts more stress on your heart than swimming (due to the way it fills up with blood in the upright position vs. the prone position). I appreciate swimming wasn't mentioned, but just thought I'd get that crack in there. 
I suppose it depends what you want to focus on: if your end objective is strength or big muscles, then running will have to give way. If you want to run like Mo Farrah, then you're going to have to accept that big muscles and ripped-ness will be somewhat beyond scope.
Practically, Stronglifts is very good for building up a good strength and muscle base. We could spend ages tailoring your workout to suit your specific needs, but at this juncture, it would be pointless.
5) Should I be taking creatine? A few runners have suggested this and I know it's popular amongst lifters too.
*Sigh* Popular myth I'm afraid. Creatine does nothing for cardiovascular/aerobic exercise. You're far better off with citrulline malate or beta alanine which play a more prominent role in aerobic activity. Creatine is popular amongst lifters because it does two things:
- It pulls water into muscles, making them look bigger;
- With correct dosing, over time, it has been shown to improve maximum muscle power output (which is pointless for runners due to the sub-maximal contractions involved).
You can see why this would be a good thing for lifters.
6) Is there anything else I should be doing (or not doing)?
Don't waste your money on glucosamine/chondritin: the evidence supporting is function is scant at best. You're far better off just taking regular fish oils and spending the money saved on something nice for your partner.
I'm open to any advice and happy to give pretty much anything a try.
