Hi justin. As someone who has trained in both Judo and Aikido my opinion, for what it's worth, is that you will find more differences than similarities between the two arts.
A good example of the different approaches is found in the ukemi waza of the two arts. Judoka tend to fall in the true sense of the word, and consequently the breakfalls are very pragmatic. Aikidoka tend to roll rather than fall, and their breakfalls are much more technically demanding. An aikidoka will look to roll back to their feet after each technique. Of course there are those that don't allow them to, but in general terms aikido uses projections rather than throws, so they can roll out of the ukemi.
In Judo, nage is usually the fulcrum around which uke is thrown. The throws involve some kind of trip (Tai otoshi, O'soto gari) or lift (O'goshi, seoi nage) from nage. In aikido, nage is the eye of a storm around which uke is propelled (irimi nage, kaiten nage) and many throws are performed off joint locks (kote gaeshi). In essence Judoka place some part of their body into uke's path, aikidoka re-direct his path and add their enegy to it. It is a little like being pushed when you run down hill as opposed to being tripped.
The locks tend to be different as well inasmuch Judo uses mainly kansetsu waza, which works against the natural movement of the joint to break it or dislocated a connected joint, whereas Aikido uses locks that more often than not go with the natural movement of the joint and extend it beyond it's normal limits.
There are many similarities as well and I think you experience of feeling your opponents energy, of kuzushi and kake, and of timing will be very beneficial to aikido training.
The biggest problem may well be in coming to terms with the different training methods. Aikido is not a fight. In the early stages of training you will no doubt come to question the validity of the attacks you recieve. That is normal, and easily explained. Aikido techniques can not be performed with full force without causing lasting injury. That is one reason why aikido is not seen in UFC and such like. It is therefore necessary for uke to "go with" the technique to avoid injury. It is also essential that you learn to feel the attack, which you can't do if it is coming at you at great speed and will knock your head off if you don't get out of the way [IMG]http://www.fightingarts.com/forums/ubb/biggrin.gif[/IMG]
Hope that is of some help.