Well done on the mileage, 3,500 miles is plenty long enough for something to have fallen off a Lotus !
The usual culprit for a vague change has already been quoted, the bushes at the bottom of the lever do wear and give a sloppy change. Not only fore/aft but also sideways movement across the gate is another symptom for that bush failing.
I'm guessing your shift linkage isn't the same as on my car (TC with 352 box) and is more likely to be one of the earlier designs with a sort of "T" pivot (Relay lever ?) in the middle and with plenty of joints in it ? If so, from looking at the arrangement in the manual perhaps there's scope for additional movement if the securing bolt has loosened off. Given you've just completed a lot of restoration work I'd be surprised if there's any wear in those pivots/bearings, I'd look for something vibrating loose over the last few months.
Likewise, if you replaced the bush at the base of the lever, it shouldn't have gone yet, it might just be the bolt working loose. Because I've got skinny arms I can get to the base of the lever through the hole in the central tunnel underneath the elbow/arm pad. If you can do the same then you'll be able to feel for free play with one hand, moving the lever with the other ? Properly adjusted there should be no discernable play between you moving the lever fore/aft/sideways and the lower rod in the tunnel.
Brian