Professa,
Maybe you could post an MP3 to let us hear what you're referring to. Now that you've given a bit more explanation, I still think that some reverb or other effects to push those instruments back a little. DIing instruments into a recorder gives a similar effect to extreme close micing.... It's in your face! So you still have to push the guitar and bass back to taste, unless the dry, in-your-face sound is what you're going for.
Mixing is also the art of blending things together, which can be difficult when you have signals from different sources. I have another thing for you to try. Try putting everything through a compressor at the end. It doesn't have to be compressing things very hard (1:5 ratio, high threshold). The idea would be to get everything to have the same sonic fingerprint by coming out of the same processor. This may be a way to blend things together.
I have another few questions: Do you record your synth parts with their effects that's on the patches in the synth(s)? When I record synth parts, I never print the effects from the synth program unless it's EXactly what I wanted (or I will turn that effects down to about halfway to leave room for options later). If you print the effects from the synth, you've already reduced your blending options. So record the synths dry if you're not doing that already. Then everything is dry and you can do all your processing from the computer and everything will probably blend better.
Rev E