The Ford 4R100 and an aftermarket control system have been a great combination in conversions and performance Ford/Ford applications for a good while. If you haven't purchased a control system yet- do your homework so you won't be disappointed. See the links below to all three manufacturers for more information. I have supported and used the PCS TCM-2000 for several years and have also worked with several using the new TCM-2800 as well. For now, I consider it the best system for the 4R100 but I could end up changing my mind since it's not perfect. For that reason I am now accepting applications for one guy to try out my new Super Shift controller with a 4R100 for a steeply discounted price. Email me through my contact form for more information if you are interested. Other systems are cheaper and maybe easier to use but not worth it in my opinion. "Easy to use" is great but when it causes limitations to what can be done with the controller it's not such a good thing.
US Shift has recently come out with the Quick 4 control system and it does have some new features that are worth a mention. It has adaptive self learn features now, but hold on- they are only for shift and lock up timing, not shift quality (firm or soft, or in the case of the 5R110 avoiding binds and flares). Shift and lock up timing is stuff that a good tuner can already adjust well with the shift point tables, so not too sure that feature will be that great for someone working with a tuner at least. The best features I see with it are the programmable shift delays and the ballistic effect which can raise shift points based on how fast the pedal is pressed.
If you need help with another system I can possibly offer support for that as well, and the Ford E4OD transmissions are similar to the 4R100, and I am quite familiar with how they are tuned with aftermarket controllers as well.