The following is a mix of personal *subjective* findings so be warned, but I maintain there's more than a little objective reasoning behind them, so tread as carefully as you like while I share how
I felt about the gear and cables
The E3 is, I believe, a souped up and externally rebodied VM95E with perhaps more careful QC from what I can see. Goldring now do an E4 stylus which I'd assume approximates the VM95EN as it has a naked decent elliptical stylus. This may be the most cost-effective 'upgrade' here. I'm a fan of the Ortofon 2M Bronze, which sounded great in a current Planar 3 (RB330 tonearm) and Ortofon now do a slimmer version especially for Rega tonearms and turntables... I'd suggest any of these options over the ND3 cartridge, which 'only' has a bonded elliptical tip for similar money to the VM95SH in the UK... To get a serious stylus upgrade, one has to go to the £300 ND5 or £400+ ND7 (Rega's Roy Gandy himself, told us that the cost to a maker of different stylus profiles wasn't very much at all, all else being equal, so make of that what you will!)
I'll say this again, as many dealers haven't an effin' clue these days about vinyl while paying lip service to it - run the Rega with lid removed completely, use the best belt Rega offer for lowest wow figures and correct the speed differences with the external power supply if it's a Neo, which offers this fine adjustment. Site the blasted thing as remote from the speakers as possible and away from corners - a lightweight isolated shelf used to work well, as does their wall bracket, which has shot up in price it seems.
The Brio R amp is 'good enough' by 1980s UK standards and sounds transparent enough, in a 'lively' kind of way. I'd suggest from first hand if sighted experience, that the phono stage and amp in general, will reproduce the subtle upgrades a 'better' turntable will give (I do like the extra emotional 'swing' and subjectively slightly more relaxed sound Planar 6 seems to add to the proceedings, but this is a purely subjective view - I like the thicker platter outer edge too and this is DEFINITELY a sight thing for me

)
I don't know the RX1's, but do know and respect the RX3 floor standing model, both offering rather more substantial cabinet builds over their predecessors and a much-needed reduction in added HF 'sparkle' which the RS3 previous generation had in abundance. Midrange on the RS and RX3, was always good I felt, the bass quality depending on room, sources and placement as much as any design consideration. Sadly, the newish Aya speaker is an objective disaster if a neutral frequency response is the ideal and two independent tests show a bumped-up 'boppy' bass at 100Hz or so, a suckout at the mid to top crossover but pleasantly neutral in between these points. Maybe they don't care, or maybe they can't measure accurately, but it's a shame, as I had high hopes for the interesting shape and enclosure material, a proper grille now added over the RX models which only partly covered the drivers from memory (my pal lost two RX3 tweeters to an over-inquisitive granddaughter poking them in!),
AHHHHH - you have RS1's.... I'd suspect a VERY 'toppy' balance with a definite added 'crispness' to them which was definitely tamed in the RX version - they don't fetch much on eht used market currently, so can you see if a set of RX1's or even RX3s can be got for well under five hundred quid?
As said above, the best 'higher fidelity' upgrade you could make (as in getting closest to the sound the mastering engineer wants you to hear), is to add a digital source. Rega's previous Apollo and Planet machines were rather hobbled frankly in a sonic-subjective sense (the DAC-R a dated design even when launched it now appears and hopelessly out of date today), a pal who loved his Apollo R upgrading to the Denon 900 machine for less money. It took him a while to emotionally let go, but he says the Denon is now judged excellent sonically, and he uses this as well as an Airport Express 2 with no qualms when switching between the two (the Apollo R always altered the sound too much, he now feels).
As for the QED cabling, I had ups and downs with their predecessors frankly, but they shouldn't veer too far from neutrality as long as they don't have silver plating in them (the Silver Anniversary award-winning stuff from yesteryear was truly dire, and I honestly don't know why, as every system it was used in suffered a kind of 'samey' flattening of dynamics and less bass power/weight, giving a 'cheap Hi-Fi' kind of 2-D sound - repeatable in various systems, rooms and dealer premises too!). The copper 79 strand, if used in not too long (say 5m maximum) runs, seemed fine here...
Hope this helps. I've tried to keep in touch with Rega products after I left the retail side of things and have tried to be as fair as I can. Using the old hierarchy situation with vinyl based systems, the speakers if you like them in your room, should happily take and reproduce 'upgrades' upstream (digital source, better pickup and deck siting and last of all, a cleaner more powerful amp choice).