Ah, spring on the San Juan! The weather is warm and the fish seem to change what they want by the hour. Fishing can be excellent during the spring but you'll have to work a little harder to dial in the rigs as Juan fish can become notoriously "column locked". Add to this a slight tinge in the water and you just have to take a guess if they are suspended mid column or down deep, unless you can see them eating high column. This is why I love the San Juan; it always keeps me on my toes and I love the day to day puzzle it presents.
Before diving into fly specifics and the thought process behind them, it is important to understand "the column". When anglers and guides talk about column they are referring to where the fish are vertically. If you split the depth into thirds you have your low column, mid column, and high column. The trout of the Juan are very much tied to the midge cycle and understanding this can set you up for success no matter what time of year. Generally in the morning before the midges and baetis begin to hatch, the fish are down deep in the lower third of the water column. Their bellies will contain things like scuds, midge larva, midge pupa, and nymphs, specifically baetis. As the temperature bumps, the fish will generally suspend in the middle of the water column and intercept the pupating midges and emerging mayflies. As the pupa become adults and the mayflies shed their exoskeleton to become dun, the fish will begin eating directly off the water's surface or just a few inches or feet below (high column). With this condensed explanation of fish and column as it relates to feeding, you'll be better armed with the tools you need to adapt to these constantly changing situations.
Things that can also affect fish and their relationship to the water column is water temperature. As the water temp drops, so does a trout's metabolism. Trout will generally want to expend less energy and you will usually find them sulking in deeper "tanks" and "holes". Deep is relative to the river or stream but on colder days, even on tailwater, I tend to focus on the deep holding lies with deep nymph rigs.
With tail water nymphing, I believe that column (depth) is the most important part of the equation. Before I change flies, I usually will change the length between my split shot and weight, and/or change split shot sizes. After depth, I think size is the most important element of your fly, then profile, then color. In no particular order, here are my favorite flies for the San Juan. These are typically fished in sizes #18-#26, with leeches and eggs #10-#18
1) Red Larva
3) Foam Back Emerger
4) KF Emerger