What Elf what hinting at is more important than you may realize, while I've yet to get to the Indigo PSU's myself. I can say that an important, unwritten, rule when dealing with capacitors in a design and what they might have been used for (filtering vs oscillation). Installing "better quality" caps can often be bad in the wrong places. Tougher filter caps (ripple tolerance), yes, better caps everywhere....no. The caps that were chosen where chosen based on data sheets. To do the design justice, you need to take a look at the caps you removed (and their original locations). You need to try your best to decode the Manufacturer, and series (family) the caps came from. Then research the manufacturer's charts and looks for the series upgrades (you may need several generations of charts...on the Indy I'm doing...I've needed TWO generations of charts to track the lineage upgrade recommendations from then to present-day.
Your jobs is to MATCH the original cap specs...not exceed them. Remember this, you're not improving the PSU, you're repairing it. Use new caps, but use caps that are similar in spec to the originals (no matter how much you may feel otherwise).
More than likely it could be something else, but for the smaller caps you found just around...it's likely to do with what you chose to replace it. Find each cap's original series data sheets (or family at least)...then go from there.
Also, just a gut reaction, lower voltage on the output side is normally a symptom of either a resistor value on your feedback circuit drifting (especially when it's literally a 1v difference in your case, like the feedback was working, but offset). In the later case of the LV side, you likely used caps that were TOO low in ESR and may have triggered a protection mechanism due to excessively out of tolerance voltage (as hinted by Elf).