S2r 800 front forks are pretty poor and they were the first thing I noticed when I bought mine, they lacked any feel and really crashed over bumps but I felt that the rear was alright if a bit soft / wallowy.
However I'm now running (occasionally!) ST4s TiN front forks and ST4s ohlins rear shock, and the difference is night and day - the forks came in a box with the bike with unknown history and the shock was bought second hand but both have been through MTC for a service and set up (stuck in a box and in the post, then returned a couple of weeks later and thrown on)
Now the bike feels a lot more settled when
on a mission allowing me (you?) to not worry about what the suspension is doing but to just press on, find a corner, chuck it in, onto the power and away to the next... Lovely and with plenty of 'feel' although it has taken a bit of time to get used to as it's like a different bike.
The ST4s rear shock is virtually the same length as stock but the back of my bike was raised about 15-20mm (static) which suggests that the original shock had too much static sag despite trying to reduce it. The only problem I have though is the 2 reservoirs for the rear shock and where to put them - I've had the hoses changed twice and I still can't get them to fit as I'd really like them to, IE hidden under the seat and out of sight so they may get hung from the frame (or it may get sold and replaced)
I do have a spare ohlins spring if you fancied changing the stock S2r one (it was cheaper / quicker for me to buy a new ohlins spring than to get the old ohlins spring powder coated) and I have read that that can make a bit of difference to the stock shock.
If you aren't adverse to moving one of the coils and cutting other bits off then other Ducati shocks can be made to fit (IE 999) relatively easily and may be another slightly cheaper option.
And for the price of a set of fork cartridges from Maxton, you could get a used set of ST4s / S4r forks, then get them serviced / re-sprung and they bolt straight in, you'd also have cash left over for a shock - I also seem to remember that GSXR600 forks could be used but it's been a while since I've looked into it and I may have had a glass of wine or 2
If I had my time again, I'd probably go with the ST4s / S4r front forks (serviced and set up) and Nitron shock without the remote reservoirs so I didn't have to fug about trying to get stuff to fit where there isn't any space, but if it were one or the other then I'd go for forks first.
If you're in the area, you're welcome to have a look at mine.