Regardless of if it came with a 1041, a 1033 or larger would be better than a 1041 because of the higher output. The 1041 was suited to set when new, without extra cars, etc. more power being available is a good thing. Find me the post that complains they bought too big a transformer and that was the issue. (assume correct wire is used,etc )
Available power vs used power; just don't come up short. Have extra on hand in case you need it.
Some things bare repeating in a different manner so you can develop a real sense of context IMO.
5v boost on old units is because the early whistle motors ate up a lot of power and that slowed the engine. So a 5v boost got added and kept it steadier; but also usually boosts speed a bit until you stop blowing it. It's really a preference more than a requirement. Some folk hate it enough they would rather it slowed down. In theory you could lessen the transformer boost internally with diodes on that tap too. I just never heard of anyone doing it.(simply splice to that wire.)
This boost or lack of it depends on transformer, new or old both. Most old had a boost, I think one or two did not.
Have you tuned up the whistle motor? It has busings, brushes and armature that need occasional attention same as a loco, just not as often unless you use the heck out of it
A tune up will likely lower the voltage it needs to get up to speed to make sound. I.e. clean and lube (and don't skip oiling BOTH bushings even though the impeller side is a pita)
Also in there, is the relay. It is a special relay that ignores ac. It triggers on dc. Specifically an offset. An ac wave has a +12v and a -12v charge that follows it. If you grab away 2v from either +/- you have 12v &10v; a 2v difference between waves.. or "2v offset". That 2v offset is either + or - in nature that is essentially +2vdc or -2vdc(if both it would remain ac), so 2vdc +or- added to +10v/-10v ac etc etc, hopefully you see the math has come full circle, lol. It being either + or - is dc , + and - both is ac, so it's dc piggy backed on ac (a dc offset)
...... so, if the relay triggers easy on the CW you are fine that is the big hurdle.. some PW relays do not like the diodes to create the offset. They fall a tiny bit short of enough offset. Some new relay boards don't like the softer curve the old whistle disks provide in the offset. (I think I've learned a trick for PW on diodes, but lets wait on that, it does have a slight drawback of a bit too much offset for motors).
. But you also say it works with more voltage applied. So tune up the whistle and try again. Note if the relay seems happy, and note how the engine reacts, then start the decision on changes like boost or voltage drops on the engine to get a happy balance (the volt drop trick can also be used to increase smoke output fyi Smoke gets full power from rollers, motor gets less )
3a may be too small for the diodes. Put the engine on the rails with a meter reading amps used. Hold it still ("stall") give it full power then back to zero fairly quickly, letting it slowly turn just enough to see amps raise to a peak, long enough to read the max amps drawn.
Use diodes larger than that peak. The more oversized, the cooler they will stay. (about 180° is the limit for heat, cooler doesn't always mean cool to the touch, but finger cool is ok too) I.e. one good peak over 3a could cook the 3a. Most of my PW peak at at least 3.5a, some at 5.5a, none use over 4.5a continuously, I use 4a and 6a on locos for voltage drops, none have cooked.
I also used a 3a to drop a voltage that was peaking at 3.8a (i didn't check). The diodes didn't burn, but got hot enough the solder failed and it fell apart repeatedly before I checked the peak (and did a tune up)
Milage may vary; but 'nuff said on diode size vs peaks?
General purpose rectifying diodes are good enough, you don't need the more expensive ones for this.