Now that you got it apart this far, it would be a shame to miss an opportunity to do a good repaint of your frame. It's really a simple car so I'm confident you can put it all back together.
If that is a bridge too far, I would find as much of the rust as you can (don't forget to look inside the 'T' and backbone), sand it away and prime and paint those areas. Usually, there is some oil coating the area around the engine so you probably won't need to pull the engine from the frame to get to those areas - but if you do, Plan A (sand blast and paint the frame) starts to make more sense.
You should replace the jute with closed cell neoprene foam (or similar). r.d. enterprises stocks this.
I would replace your shocks and springs. Richard at Banks recommends 250# front and 130# to 150# rear. That sounds very high but in reality, those spring rates work very well and are not at all uncomfortable. He sells them as well as some nice shocks. r.d. and Dave Bean also sell good shocks. I'm not sure they are on board with Richard's spring recommendation, but I don't know.
You may want to replace the rear bearings and replace the spacers with hardened steel replacements. I don't think this is as critical as it is with S2s, but you've gone this far, you might as well freshen them, too.
Depending on your budget, you may want to consider Richard's twin link rear suspension, rear disc brake, and/or vented front disc brake. Adjustable front A-arms are a good idea. The stock setup was designed to be destroyed in a crash to help save your frame. If your A-arm pieces are straight, you might consider replacing the top ones with adjustable units and leave the bottom ones as they are more likely to be damaged. They're getting rare so at some point, we'll all probably end up with tubular units. Adjustable rear links are also a good idea. It would probably be a good idea to replace the front suspension bushings with polyurethane units. This looks like a good place to get them:
http://www.autobush.com/8/Lotus/Elan-Twin-CamJust my $0.02!