So I think I've interpreted your question correctly. If not, fire away in the comments.
Confusingly there are several factors in diffie hellman: are you doing it over elliptic curves or not, what size group have you got (let's assume "strong" and "not strong") and whether you generate ephemeral private/public keypairs or not.
The problem with logjam is this: if you have a plain old group variant of DHE, then if you can persuade the server to downgrade to the export (weak variety) level strength, then with some precomputations made before you can break the secret generated for a session in minutes.
This is conditional on being able to downgrade size variable to a smaller one - if you can do this over the plain old DHE variant, then you're in business.
This requires the cipher suite have
DHE_..._EXPORT_... in it, such as
TLS_DHE_DSS_EXPORT_WITH_DES40_CBC_SHA. Now that has a bunch of other problems like 40-bit DES and whatnot, but essentially, there could feasibly be some servers out there that support EXPORT variants of DHE with better symmetric ciphers. Or they could actually be negotiating 40-bit DES if persuaded.
The point is to perform a downgrade attack. The cipher suite list you've given doesn't allow for export ciphers.
You could turn off all non-EC variants of DH. However, this might limit client side support. Whether or not you can be so limiting is really up to you. But "DHE" in and of itself is fine, unless there's export in there somewhere. Make sure export ciphers are disabled, and follow Thomas' advice in the answer you linked.
Now on to
SSLDHParametersFile - in DHE, the prime and generator of the group can actually be fixed ahead of time - the bit that is ephemeral is the private key chosen in that group. This way, by setting the parameters you can control what size group your server uses.
For example, the output of this might be:
openssl dhparam 2048 -text
PKCS#3 DH Parameters: (2048 bit)
generator: 2 (0x2)
Tellingly, from your example bug, it sounds like it is not possible to use these parameter files quite yet with Tomcat. I'm not an expert on Tomcat, so, I can't really say but if you have instructed the cipher suites to not allow export, OpenSSL should default to a 1024-bit DH group, which is good enough for now.
You can, then, when the patch is available, upgrade your DH parameters as you see fit.