Had a chance to look through your synth at last; not had time to delve in much detail, but here's my first impressions.
Sorry to sound like your Parent/Spouse/Policeman etc., but it could really do with a bit of a tidy up - all the links that criss-cross and go over/under modules make it tricky to see what's going on. You'll most likely see a lot of the problems yourself once the routing is neater. It also makes it easier to get help on the forum coz people can find their way around easier.
Most of your routiing problems seem to be similar...
All the white poly connections in SM look the same, and SM treats them all the same way - but for a synth designer there are really two kinds of poly signal and it's the designer's job to know which is which.
Type 1) The synth's audio - any poly link carrying an actual sound. On most modules the top input/outputs (usually just called 'in' and out') carry the sound itself.
Type 2) Control Signals - these aren't sounds, but are the signals telling the synth what to do
to the sound. For example, the output of an Knob, LFO or Envelope, or the signals from the MIDI to Poly. An input on a module that you might normally connect a knob to is expecting a control signal.
I see a few places in your synth where the two are being mixed in odd ways...
'To Amp Env' on the sequencer is plugged into the 'In' of the ADSR - the 'In' on the ADSR should take only the audio that you want to do an envelope on - 'To Amp Env' is a control signal, most likely for the envelope amount (multiply it with one of the VCA Levels inside the ADSR module).
The Sequencer module takes an input from the filter - but the filter output is an audio signal, so not really something that you can directly control sequencer parameters with.
The way I would tackle it would be to arrange all of the modules/links that carry the audio
together in a line, from Osc>>Filter>Amp Env>>Combiner>>Delay All the remaining modules then hang off the side of the line of audio modules, feeding them with control signals.
Here's a link to the best Synth resource I've ever found - there's no programming tips or SM stuff, it just really explains what everything inside a synth is there for (Part 3 is a good explanation of control signals and modulation)http://www.soundonsound.com/sos/allsynthsecrets.htm
Of course, like all rules, there are plenty of grey areas and exceptions - so don't stop the experimenting, some very weird and wonderful things have been discovered that way too...