Just a short list of quick thoughts / speculation. Probably things you've already contemplated / checked. If you cut over the DNS does the lesser VPS still keep up (or does it start to lag)?
Similiar load on both sites (connections, end users, etc)? Same server farm (and network) for both VPS? Same underlying OS / configuration / optimizations? Same PHP <==> HTTP server setup? Any noticeable pattern looking at page parse / SQL times between the two? Is one noticeably slower when writing to the DB via Zen Cart (possibly test using EZ Populate or similiar)? Any "security" software on either? Any proxy / cache / CDN setups? Any "limiting" or QOS? Any output filters (PHP or HTTPd)? Similiar physical hardware for both hosts (CPU, mem, hdd - speed, latency, bandwidth, etc)?
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