Is it possible to avoid a ~$40 fee for a 220-input transaction?
bitcoinfees.21.co shows that fees are fairly low currently. You may try to export keys from your old electrum wallet, and load them into a new Electrum wallet (then you don't need to "transfer"), and go from there. The newer version allows to set tx fees in Saoshi/Byte. 
Alternativly:
If you are on OpenBSD, Linux or MAC, you could give it a try with these shell scripts: github.com/pebwindkraft/trx_cl_suite (you don't want to provide your private keys or similiar to anyone!). 
I used the tools last recently to create manually a tx (c9908124e59a2794f3807b366be7d235ff7654251adcdf396e209236341‌​b3c32) with 20 Satoshis per Byte, having a size of 18KBytes.