By the time chassis 26/4109 rolled off the production line a few weeks later, the entire selection of new parts were on stream. This included new front brake calipers with larger diameter pistons, a new brake master cylinder, a new clutch master cylinder, revised rear brake discs, revised differential and new intermediate and outboard shafts. From chassis 26/4127 the new one-piece rear light clusters were also fitted whilst later on, the battery was sensibly moved from behind the passenger seat to the left-hand side of the boot.

Later in S2 production, two more optional upgrades were offered to Elan buyers, the first comprising a set of centre-locking steel wheels in place of the existing quadruple bolt-on arrangement. There was also the advent of the Special Equipment (SE) package introduced in January 1966. The SE featured new carburettor chokes and jets plus high lift camshafts that upped peak output to 115bhp at 6000rpm. The close-ratio gearbox came as standard on all SE's along with servo-assisted brakes for the first time. SE's occasionally came with a distinctive centre stripe as depicted above, the additional 10bhp providing a useful boost in performance. Top speed rose to 120mph while 0-60 dropped to comfortably under seven seconds.

Whilst most SE's were equipped as such from new, some earlier cars were brought up to Special Equipment configuration. All SE's featured a green Lotus cylinder head in place of the standard blue item. The last S2 built was chassis 26/5810 in June 1966 but because of the non-sequential numbering system, it is believed that somewhere in the region 1300 were actually produced.